Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/inputs/xbv Working: n-1-126.cluster.ucsf.bkslab.org:/scratch/xiaobo/2379/xbv-8058097.48 Result: /scratch/xiaobo/2379/xbv-8058097.48 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xbv 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/xbv mkdir: created directory `/scratch/xiaobo/2379' mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48' /scratch/xiaobo/2379/xbv-8058097.48 /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/2379/xbv-8058097.48/working' mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/protonate' Storing results in /scratch/xiaobo/2379/xbv-8058097.48/finished Working in /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 /scratch/xiaobo/2379/xbv-8058097.48/working/protonate /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Using inputs as protomers/tautomers. No processing done 480 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/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Bulk generating 3D conformations all protomers in /scratch/xiaobo/2379/xbv-8058097.48/working/3D mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/2379/xbv-8058097.48/working/protonate/xbv-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 ZINC001338071628 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building' mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338071628 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/1 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)C1) `ZINC001338071628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338071628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338071628 none CC(=O)N1CC(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 50, 40, 40, 20, 15, 20, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 40, 50, 50, 50, 40, 40, 40, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 40, 40] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/2 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)C1) `ZINC001338071628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338071628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338071628 none CC(=O)N1CC(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 50, 34, 34, 19, 15, 19, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 34, 50, 50, 50, 34, 34, 34, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 34, 34] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338071628 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/finished' Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628 Building ZINC001338071628 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338071628 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 1) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(=O)N1CC(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)C1) `ZINC001338071628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338071628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338071628 none CC(=O)N1CC(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 50, 40, 40, 20, 15, 20, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 40, 50, 50, 50, 40, 40, 40, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 40, 40] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 2) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(=O)N1CC(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)C1) `ZINC001338071628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338071628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338071628 none CC(=O)N1CC(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 50, 34, 34, 19, 15, 19, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 34, 50, 50, 50, 34, 34, 34, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 34, 34] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338071628 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338071628 Building ZINC001338088590 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338088590 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/3 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338088590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088590 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 17, 17, 38, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/4 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/4' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338088590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088590 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 16, 16, 39, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338088590 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590 Building ZINC001338088590 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338088590 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 3) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338088590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088590 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 17, 17, 38, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 4) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338088590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088590 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 16, 16, 39, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338088590 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088590 Building ZINC001338088591 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338088591 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/5 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338088591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088591 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 15, 15, 42, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 42, 42, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/6 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338088591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088591 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 14, 14, 48, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 48, 48, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338088591 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591 Building ZINC001338088591 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338088591 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 5) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338088591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088591 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 15, 15, 42, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 42, 42, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 6) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338088591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088591 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 14, 14, 48, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 48, 48, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338088591 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088591 Building ZINC001338088592 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338088592 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/7 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338088592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088592 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 14, 14, 48, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 48, 48, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/8 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338088592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088592 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 14, 14, 42, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 42, 42, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338088592 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592 Building ZINC001338088592 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338088592 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 7) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338088592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088592 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 14, 14, 48, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 48, 48, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 8) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338088592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088592 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 14, 14, 42, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 42, 42, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338088592 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088592 Building ZINC001338088593 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338088593 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/9 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338088593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088593 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 16, 16, 39, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/10 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338088593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088593 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 17, 17, 38, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338088593 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593 Building ZINC001338088593 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338088593 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 9) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338088593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088593 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 16, 16, 39, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 10) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O) `ZINC001338088593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338088593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338088593 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 17, 17, 38, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338088593 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338088593 Building ZINC001338099051 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338099051 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/11 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2NS(C)(=O)=O)cn1) `ZINC001338099051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338099051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001338099051 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2NS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 14, 26, 26, 22, 26, 26, 26, 34, 36, 36, 36, 5, 5, 5, 5, 5, 5, 2, 14, 14, 26, 26, 26, 26, 34, 36, 36, 36, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/12 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccccc2NS(C)(=O)=O)cn1) `ZINC001338099051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338099051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001338099051 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccccc2NS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 14, 27, 27, 27, 27, 27, 27, 34, 35, 35, 35, 5, 5, 5, 5, 5, 5, 2, 14, 14, 27, 27, 27, 27, 34, 35, 35, 35, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338099051 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051 Building ZINC001338099051 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338099051 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 11) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2NS(C)(=O)=O)cn1) `ZINC001338099051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338099051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001338099051 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2NS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 14, 26, 26, 22, 26, 26, 26, 34, 36, 36, 36, 5, 5, 5, 5, 5, 5, 2, 14, 14, 26, 26, 26, 26, 34, 36, 36, 36, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 12) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccccc2NS(C)(=O)=O)cn1) `ZINC001338099051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338099051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001338099051 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccccc2NS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 14, 27, 27, 27, 27, 27, 27, 34, 35, 35, 35, 5, 5, 5, 5, 5, 5, 2, 14, 14, 27, 27, 27, 27, 34, 35, 35, 35, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338099051 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338099051 Building ZINC001338104957 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338104957 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/13 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncn(Cc2cccnc2)n1) `ZINC001338104957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338104957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338104957 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncn(Cc2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 20, 46, 46, 46, 46, 46, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 20, 20, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/14 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncn(Cc2cccnc2)n1) `ZINC001338104957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338104957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338104957 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncn(Cc2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 19, 45, 45, 45, 45, 45, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 19, 19, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338104957 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957 Building ZINC001338104957 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338104957 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 13) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncn(Cc2cccnc2)n1) `ZINC001338104957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338104957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338104957 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncn(Cc2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 20, 46, 46, 46, 46, 46, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 20, 20, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 14) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncn(Cc2cccnc2)n1) `ZINC001338104957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338104957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338104957 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncn(Cc2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 19, 45, 45, 45, 45, 45, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 19, 19, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338104957 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338104957 Building ZINC001338119344 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338119344 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/15 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338119344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119344 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 15, 15, 36, 39, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 36, 36, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/16 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338119344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119344 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 33, 37, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33, 37, 37, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338119344 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344 Building ZINC001338119344 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338119344 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 15) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338119344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119344 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 15, 15, 36, 39, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 36, 36, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 16) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338119344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119344 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 33, 37, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33, 37, 37, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338119344 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119344 Building ZINC001338119345 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338119345 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/17 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338119345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119345 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 34, 38, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 34, 34, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/18 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338119345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119345 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 14, 14, 35, 39, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 35, 35, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338119345 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345 Building ZINC001338119345 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338119345 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 17) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338119345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119345 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 34, 38, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 34, 34, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 18) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338119345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119345 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 14, 14, 35, 39, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 35, 35, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338119345 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119345 Building ZINC001338119346 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338119346 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/19 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338119346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119346 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 34, 38, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 34, 34, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/20 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338119346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119346 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 33, 38, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33, 33, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338119346 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346 Building ZINC001338119346 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338119346 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 19) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338119346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119346 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 34, 38, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 34, 34, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 20) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338119346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119346 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 33, 38, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33, 33, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338119346 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119346 Building ZINC001338119347 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338119347 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/21 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338119347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119347 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 33, 38, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33, 33, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/22 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338119347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119347 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 13, 13, 35, 38, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338119347 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347 Building ZINC001338119347 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338119347 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 21) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338119347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119347 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 33, 38, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33, 33, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 22) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1) `ZINC001338119347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338119347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338119347 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 13, 13, 35, 38, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338119347 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338119347 Building ZINC001338129103 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338129103 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/23 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1) `ZINC001338129103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338129103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129103 none COc1nccc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 18, 14, 18, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/24 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1) `ZINC001338129103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338129103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129103 none COc1nccc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 19, 16, 19, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338129103 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103 Building ZINC001338129103 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338129103 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 23) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1nccc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1) `ZINC001338129103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338129103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129103 none COc1nccc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 18, 14, 18, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 24) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1nccc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1) `ZINC001338129103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338129103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129103 none COc1nccc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 19, 16, 19, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338129103 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129103 Building ZINC001338129106 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338129106 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/25 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1) `ZINC001338129106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338129106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129106 none COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 20, 16, 20, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/26 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1) `ZINC001338129106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338129106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129106 none COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 18, 14, 18, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338129106 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106 Building ZINC001338129106 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338129106 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 25) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1) `ZINC001338129106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338129106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129106 none COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 20, 16, 20, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 26) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1) `ZINC001338129106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338129106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129106 none COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 18, 14, 18, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338129106 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129106 Building ZINC001338129108 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338129108 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/27 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1) `ZINC001338129108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338129108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129108 none COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 19, 16, 19, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/28 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/28' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1) `ZINC001338129108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338129108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129108 none COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 17, 13, 17, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338129108 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108 Building ZINC001338129108 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338129108 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 27) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1) `ZINC001338129108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338129108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129108 none COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 19, 16, 19, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 28) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1) `ZINC001338129108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338129108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129108 none COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 17, 13, 17, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338129108 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129108 Building ZINC001338129111 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338129111 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/29 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1) `ZINC001338129111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338129111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129111 none COc1nccc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 17, 13, 17, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/30 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1) `ZINC001338129111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338129111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129111 none COc1nccc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 18, 14, 18, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338129111 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111 Building ZINC001338129111 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338129111 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 29) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1nccc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1) `ZINC001338129111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338129111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129111 none COc1nccc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 17, 13, 17, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 30) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1nccc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1) `ZINC001338129111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338129111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338129111 none COc1nccc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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, 18, 14, 18, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338129111 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338129111 Building ZINC001338130683 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338130683 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/31 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338130683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130683 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/32 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338130683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130683 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 30, 30, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338130683 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683 Building ZINC001338130683 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338130683 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 31) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338130683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130683 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 32) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338130683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130683 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 30, 30, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338130683 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130683 Building ZINC001338130684 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338130684 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/33 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338130684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130684 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 29, 29, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/34 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338130684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130684 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338130684 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684 Building ZINC001338130684 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338130684 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 33) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338130684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130684 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 29, 29, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 34) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338130684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130684 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338130684 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130684 Building ZINC001338130685 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338130685 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/35 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338130685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130685 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 30, 30, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/36 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338130685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130685 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 30, 30, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338130685 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685 Building ZINC001338130685 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338130685 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 35) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338130685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130685 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 30, 30, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 36) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338130685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130685 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 30, 30, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338130685 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130685 Building ZINC001338130686 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338130686 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/37 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338130686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130686 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 30, 30, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/38 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338130686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130686 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 30, 30, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338130686 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686 Building ZINC001338130686 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338130686 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 37) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338130686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130686 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 30, 30, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 38) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O) `ZINC001338130686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338130686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338130686 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 30, 30, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338130686 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338130686 Building ZINC001338134357 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338134357 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/39 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338134357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134357 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 12, 12, 42, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 42, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/40 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338134357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134357 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 13, 13, 43, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/2379/xbv-8058097.48/working/building/ZINC001338134357 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338134357 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357 Building ZINC001338134357 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338134357 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 39) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338134357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134357 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 12, 12, 42, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 42, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 40) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338134357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134357 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 13, 13, 43, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/2379/xbv-8058097.48/working/building/ZINC001338134357 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338134357 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134357 Building ZINC001338134359 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338134359 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/41 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338134359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134359 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 13, 13, 42, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 42, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/42 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/42' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338134359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134359 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 12, 12, 41, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/2379/xbv-8058097.48/working/building/ZINC001338134359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338134359 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359 Building ZINC001338134359 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338134359 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 41) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338134359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134359 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 13, 13, 42, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 42, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 42) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338134359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134359 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 12, 12, 41, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/2379/xbv-8058097.48/working/building/ZINC001338134359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338134359 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134359 Building ZINC001338134360 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338134360 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/43 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338134360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134360 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 14, 14, 35, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/44 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338134360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134360 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 15, 15, 40, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/2379/xbv-8058097.48/working/building/ZINC001338134360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338134360 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360 Building ZINC001338134360 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338134360 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 43) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338134360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134360 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 14, 14, 35, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 44) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338134360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134360 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 15, 15, 40, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/2379/xbv-8058097.48/working/building/ZINC001338134360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338134360 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134360 Building ZINC001338134362 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338134362 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/45 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338134362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134362 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 15, 15, 40, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/2379/xbv-8058097.48/working/building/ZINC001338134362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/46 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338134362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134362 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 14, 14, 35, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338134362 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362 Building ZINC001338134362 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338134362 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 45) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338134362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134362 none C[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 15, 15, 40, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/2379/xbv-8058097.48/working/building/ZINC001338134362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 46) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C) `ZINC001338134362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338134362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338134362 none C[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)Cc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 14, 14, 35, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338134362 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338134362 Building ZINC001338146300 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338146300 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/47 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1) `ZINC001338146300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338146300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146300 none CCn1cc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 19, 15, 19, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 38, 38, 50, 50, 50, 50, 50, 38, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/48 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1) `ZINC001338146300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338146300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146300 none CCn1cc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 18, 16, 18, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 40, 40, 50, 50, 50, 50, 50, 40, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338146300 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300 Building ZINC001338146300 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338146300 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 47) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1) `ZINC001338146300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338146300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146300 none CCn1cc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 19, 15, 19, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 38, 38, 50, 50, 50, 50, 50, 38, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 48) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1) `ZINC001338146300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338146300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146300 none CCn1cc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 18, 16, 18, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 40, 40, 50, 50, 50, 50, 50, 40, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338146300 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146300 Building ZINC001338146301 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338146301 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/49 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1) `ZINC001338146301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338146301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146301 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 17, 14, 17, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 34, 34, 50, 50, 50, 50, 50, 34, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/50 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1) `ZINC001338146301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338146301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146301 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 20, 13, 20, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 38, 38, 50, 50, 50, 50, 50, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338146301 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301 Building ZINC001338146301 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338146301 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 49) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1) `ZINC001338146301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338146301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146301 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 17, 14, 17, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 34, 34, 50, 50, 50, 50, 50, 34, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 50) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1) `ZINC001338146301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338146301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146301 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 20, 13, 20, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 38, 38, 50, 50, 50, 50, 50, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338146301 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146301 Building ZINC001338146302 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338146302 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/51 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1) `ZINC001338146302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338146302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146302 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 19, 16, 19, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 39, 39, 50, 50, 50, 50, 50, 39, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/52 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1) `ZINC001338146302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338146302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146302 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 19, 15, 19, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 38, 38, 50, 50, 50, 50, 50, 38, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338146302 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302 Building ZINC001338146302 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338146302 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 51) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1) `ZINC001338146302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338146302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146302 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 19, 16, 19, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 39, 39, 50, 50, 50, 50, 50, 39, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 52) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1) `ZINC001338146302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338146302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146302 none CCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 19, 15, 19, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 38, 38, 50, 50, 50, 50, 50, 38, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338146302 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146302 Building ZINC001338146303 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338146303 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/53 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1) `ZINC001338146303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338146303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146303 none CCn1cc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 21, 13, 21, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 38, 38, 50, 50, 50, 50, 50, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/54 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1) `ZINC001338146303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338146303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146303 none CCn1cc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 18, 15, 18, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 35, 35, 50, 50, 50, 50, 50, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338146303 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303 Building ZINC001338146303 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338146303 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 53) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1) `ZINC001338146303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338146303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146303 none CCn1cc(C(=O)N2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 21, 13, 21, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 38, 38, 50, 50, 50, 50, 50, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 54) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1) `ZINC001338146303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338146303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001338146303 none CCn1cc(C(=O)N2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 18, 15, 18, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 35, 35, 50, 50, 50, 50, 50, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338146303 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338146303 Building ZINC001338151839 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338151839 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/55 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC001338151839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338151839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001338151839 none COC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 25, 36, 8, 8, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 8, 36, 36, 36, 25, 8, 8, 8, 4, 5, 5, 4, 5, 5, 4, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/56 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC001338151839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338151839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001338151839 none COC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 26, 36, 7, 7, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 36, 36, 36, 26, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338151839 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839 Building ZINC001338151839 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338151839 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 55) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC001338151839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338151839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001338151839 none COC(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 25, 36, 8, 8, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 8, 36, 36, 36, 25, 8, 8, 8, 4, 5, 5, 4, 5, 5, 4, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 56) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC001338151839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338151839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001338151839 none COC(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['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.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 26, 36, 7, 7, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 36, 36, 36, 26, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338151839 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338151839 Building ZINC001338176051 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338176051 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/57 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338176051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338176051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176051 none Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 15, 34, 15, 15, 15, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/58 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338176051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338176051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176051 none Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 14, 34, 14, 14, 14, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 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/2379/xbv-8058097.48/working/building/ZINC001338176051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338176051 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051 Building ZINC001338176051 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338176051 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 57) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338176051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338176051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176051 none Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 15, 34, 15, 15, 15, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 58) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338176051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338176051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176051 none Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 14, 34, 14, 14, 14, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 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/2379/xbv-8058097.48/working/building/ZINC001338176051 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338176051 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176051 Building ZINC001338176056 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338176056 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/59 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338176056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338176056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176056 none Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 14, 35, 14, 14, 14, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 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/2379/xbv-8058097.48/working/building/ZINC001338176056 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/60 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/60' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338176056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338176056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176056 none Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 15, 34, 15, 15, 15, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338176056 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056 Building ZINC001338176056 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338176056 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 59) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338176056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338176056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176056 none Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 14, 35, 14, 14, 14, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 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/2379/xbv-8058097.48/working/building/ZINC001338176056 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 60) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338176056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338176056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176056 none Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 15, 34, 15, 15, 15, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338176056 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176056 Building ZINC001338176059 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338176059 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/61 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338176059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338176059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176059 none Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 22, 6, 22, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 49, 49, 49, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6] 49 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/62 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338176059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338176059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176059 none Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 8, 26, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 50, 50, 50, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338176059 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059 Building ZINC001338176059 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338176059 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 61) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338176059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338176059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176059 none Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 22, 6, 22, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 49, 49, 49, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6] 49 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 62) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338176059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338176059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176059 none Cc1nn[nH]c1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 8, 26, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 50, 50, 50, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338176059 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176059 Building ZINC001338176062 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338176062 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/63 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338176062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338176062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176062 none Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 7, 25, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 50, 50, 50, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/64 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/64' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338176062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338176062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176062 none Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 26, 6, 26, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 48, 48, 48, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6] 48 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338176062 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062 Building ZINC001338176062 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338176062 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 63) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338176062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338176062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176062 none Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 7, 25, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 50, 50, 50, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 64) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338176062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338176062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338176062 none Cc1nn[nH]c1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 26, 6, 26, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 48, 48, 48, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6] 48 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338176062 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338176062 Building ZINC001338181922 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338181922 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/65 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338181922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338181922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181922 none Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 14, 34, 14, 14, 14, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/66 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338181922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338181922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181922 none Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 15, 34, 15, 15, 15, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338181922 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922 Building ZINC001338181922 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338181922 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 65) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338181922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338181922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181922 none Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 14, 34, 14, 14, 14, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 66) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338181922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338181922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181922 none Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 15, 34, 15, 15, 15, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338181922 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181922 Building ZINC001338181923 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338181923 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/67 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338181923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338181923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181923 none Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 24, 6, 24, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 50, 50, 50, 50, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/68 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338181923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338181923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181923 none Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 23, 6, 23, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 50, 50, 50, 50, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338181923 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923 Building ZINC001338181923 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338181923 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 67) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338181923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338181923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181923 none Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 24, 6, 24, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 50, 50, 50, 50, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 68) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338181923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338181923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181923 none Cn1nncc1C(=O)N1CC[C@@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 23, 6, 23, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 50, 50, 50, 50, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338181923 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181923 Building ZINC001338181924 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338181924 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/69 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338181924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338181924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181924 none Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 22, 6, 22, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 50, 50, 50, 50, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/70 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338181924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338181924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181924 none Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 26, 7, 26, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 50, 50, 50, 50, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338181924 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924 Building ZINC001338181924 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338181924 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 69) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338181924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338181924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181924 none Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 22, 6, 22, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 50, 50, 50, 50, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 70) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12) `ZINC001338181924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338181924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181924 none Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 26, 7, 26, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 50, 50, 50, 50, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338181924 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181924 Building ZINC001338181925 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338181925 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/71 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338181925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338181925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181925 none Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 16, 34, 16, 16, 16, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/72 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338181925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338181925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181925 none Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 14, 35, 14, 14, 14, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338181925 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925 Building ZINC001338181925 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338181925 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 71) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338181925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338181925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181925 none Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 16, 34, 16, 16, 16, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 72) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12) `ZINC001338181925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338181925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338181925 none Cn1nncc1C(=O)N1CC[C@]2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 14, 35, 14, 14, 14, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338181925 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338181925 Building ZINC001338258247 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338258247 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/73 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C) `ZINC001338258247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338258247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001338258247 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 13, 13, 11, 13, 13, 11, 8, 20, 20, 20, 20, 20, 8, 8, 8, 5, 11, 13, 13, 11, 13, 13, 11, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/74 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C) `ZINC001338258247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338258247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001338258247 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 14, 14, 11, 14, 14, 11, 8, 20, 20, 20, 20, 20, 8, 8, 8, 5, 11, 14, 14, 11, 14, 14, 11, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338258247 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247 Building ZINC001338258247 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338258247 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 73) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/73: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C) `ZINC001338258247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338258247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001338258247 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 13, 13, 11, 13, 13, 11, 8, 20, 20, 20, 20, 20, 8, 8, 8, 5, 11, 13, 13, 11, 13, 13, 11, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 74) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C) `ZINC001338258247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338258247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001338258247 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 14, 14, 11, 14, 14, 11, 8, 20, 20, 20, 20, 20, 8, 8, 8, 5, 11, 14, 14, 11, 14, 14, 11, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338258247 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258247 Building ZINC001338258248 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338258248 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/75 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C) `ZINC001338258248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338258248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001338258248 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 14, 14, 11, 14, 14, 11, 8, 20, 20, 20, 20, 20, 8, 8, 8, 5, 11, 14, 14, 11, 14, 14, 11, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/76 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/76' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C) `ZINC001338258248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338258248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001338258248 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 13, 13, 11, 13, 13, 11, 8, 20, 20, 20, 20, 20, 8, 8, 8, 5, 11, 13, 13, 13, 13, 13, 11, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338258248 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248 Building ZINC001338258248 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338258248 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 75) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C) `ZINC001338258248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338258248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001338258248 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 14, 14, 11, 14, 14, 11, 8, 20, 20, 20, 20, 20, 8, 8, 8, 5, 11, 14, 14, 11, 14, 14, 11, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 76) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C) `ZINC001338258248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338258248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001338258248 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 13, 13, 11, 13, 13, 11, 8, 20, 20, 20, 20, 20, 8, 8, 8, 5, 11, 13, 13, 13, 13, 13, 11, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338258248 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338258248 Building ZINC001338261795 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261795 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/77 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261795 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 25, 25, 41, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 41, 41, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 172 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/78 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/78' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261795 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 25, 25, 42, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 42, 42, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 160 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261795 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795 Building ZINC001338261795 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261795 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 77) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261795 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 25, 25, 41, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 41, 41, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 172 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 78) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261795 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 25, 25, 42, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 42, 42, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 160 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261795 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261795 Building ZINC001338261797 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261797 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/79 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261797 none C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 24, 24, 40, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 40, 40, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/80 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261797 none C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 18, 18, 35, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 35, 35, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 158 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261797 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797 Building ZINC001338261797 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261797 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 79) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261797 none C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 24, 24, 40, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 40, 40, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 80) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261797 none C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 18, 18, 35, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 35, 35, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 158 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261797 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261797 Building ZINC001338261799 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261799 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/81 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261799 none C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 41, 50, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 41, 41, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/82 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261799 none C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 18, 18, 38, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 38, 38, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261799 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799 Building ZINC001338261799 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261799 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 81) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261799 none C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 41, 50, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 41, 41, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 82) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261799 none C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 18, 18, 38, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 38, 38, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261799 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261799 Building ZINC001338261801 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261801 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/83 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261801 none C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 40, 50, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 40, 40, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/84 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/84' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261801 none C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 4, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 38, 50, 50, 50, 50, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 38, 38, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 160 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261801 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801 Building ZINC001338261801 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261801 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 83) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261801 none C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 40, 50, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 40, 40, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 84) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1) `ZINC001338261801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338261801 none C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCN1C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 4, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 38, 50, 50, 50, 50, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 38, 38, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 160 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261801 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261801 Building ZINC001338261883 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261883 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/85 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338261883.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261883 none CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 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, 18, 8, 18, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 43, 43, 8, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 182 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/86 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338261883.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261883 none CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 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, 19, 8, 19, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 43, 43, 8, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 184 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261883 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883 Building ZINC001338261883 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261883 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 85) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338261883.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261883 none CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 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, 18, 8, 18, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 43, 43, 8, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 182 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 86) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338261883.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261883 none CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 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, 19, 8, 19, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 43, 43, 8, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 184 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261883 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261883 Building ZINC001338261887 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261887 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/87 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338261887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261887 none CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 21, 9, 21, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 43, 43, 9, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 194 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/88 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338261887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261887 none CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 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, 27, 11, 27, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 49, 49, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 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: 198 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261887 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887 Building ZINC001338261887 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261887 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 87) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338261887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261887 none CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 21, 9, 21, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 43, 43, 9, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 194 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 88) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338261887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261887 none CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 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, 27, 11, 27, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 49, 49, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 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: 198 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261887 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261887 Building ZINC001338261891 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261891 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/89 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338261891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261891 none CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 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, 18, 10, 18, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 32, 32, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/90 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338261891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261891 none CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 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, 19, 11, 19, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 39, 39, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261891 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891 Building ZINC001338261891 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261891 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 89) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338261891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261891 none CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 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, 18, 10, 18, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 32, 32, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 90) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338261891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261891 none CNC(=O)CC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 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, 19, 11, 19, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 39, 39, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261891 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261891 Building ZINC001338261895 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261895 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/91 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338261895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261895 none CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 21, 9, 21, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 43, 43, 9, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 183 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/92 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338261895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261895 none CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 16, 9, 16, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 36, 36, 9, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 185 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261895 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895 Building ZINC001338261895 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338261895 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 91) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338261895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338261895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261895 none CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 21, 9, 21, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 43, 43, 9, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 183 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 92) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338261895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338261895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338261895 none CNC(=O)CC(=O)N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 16, 9, 16, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 36, 36, 9, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 185 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338261895 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338261895 Building ZINC001338282531 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338282531 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/93 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338282531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338282531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282531 none CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 45, 50, 35, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 46, 35, 35, 6, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/94 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338282531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338282531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282531 none CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 33, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 46, 33, 33, 9, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338282531 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531 Building ZINC001338282531 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338282531 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 93) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338282531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338282531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282531 none CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 45, 50, 35, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 46, 35, 35, 6, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 94) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338282531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338282531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282531 none CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 33, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 46, 33, 33, 9, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338282531 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282531 Building ZINC001338282533 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338282533 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/95 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338282533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338282533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282533 none CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 9, 9, 9, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 38, 38, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/96 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338282533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338282533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282533 none CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 50, 50, 50, 50, 50, 37, 37, 9, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338282533 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533 Building ZINC001338282533 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338282533 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 95) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338282533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338282533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282533 none CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 9, 9, 9, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 38, 38, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 96) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001338282533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338282533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282533 none CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 50, 50, 50, 50, 50, 37, 37, 9, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338282533 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282533 Building ZINC001338282535 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338282535 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/97 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338282535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338282535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282535 none CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 27, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 46, 27, 27, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 33, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/98 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338282535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338282535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282535 none CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 28, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 45, 28, 28, 6, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338282535 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535 Building ZINC001338282535 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338282535 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 97) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338282535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338282535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282535 none CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 27, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 46, 27, 27, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 33, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 98) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338282535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338282535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282535 none CNC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 28, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 45, 28, 28, 6, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338282535 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282535 Building ZINC001338282537 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338282537 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/99 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338282537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338282537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282537 none CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 11, 11, 11, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 36, 36, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/100 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338282537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338282537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282537 none CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 38, 38, 10, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338282537 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537 Building ZINC001338282537 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338282537 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 99) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338282537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338282537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282537 none CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 11, 11, 11, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 36, 36, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 100) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001338282537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338282537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338282537 none CNC(=O)NCC(=O)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 38, 38, 10, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338282537 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338282537 Building ZINC001338325242 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338325242 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/101 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338325242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325242 none CC(=O)N(C)CC(=O)N[C@@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 45, 45, 29, 29, 29, 29, 29, 10, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 45, 29, 29, 29, 29, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/102 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338325242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325242 none CC(=O)N(C)CC(=O)N[C@@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 44, 44, 44, 30, 30, 30, 30, 30, 9, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 50, 49, 49, 44, 30, 30, 30, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30] 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: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338325242 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242 Building ZINC001338325242 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338325242 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 101) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(=O)N(C)CC(=O)N[C@@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338325242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325242 none CC(=O)N(C)CC(=O)N[C@@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 45, 45, 29, 29, 29, 29, 29, 10, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 45, 29, 29, 29, 29, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 102) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(=O)N(C)CC(=O)N[C@@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338325242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325242 none CC(=O)N(C)CC(=O)N[C@@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 44, 44, 44, 30, 30, 30, 30, 30, 9, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 50, 49, 49, 44, 30, 30, 30, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30] 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: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338325242 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325242 Building ZINC001338325243 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338325243 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/103 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338325243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325243 none CC(=O)N(C)CC(=O)N[C@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 50, 34, 34, 34, 23, 23, 23, 23, 23, 17, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 47, 47, 34, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/104 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338325243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325243 none CC(=O)N(C)CC(=O)N[C@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 37, 37, 37, 25, 25, 25, 25, 25, 17, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 49, 49, 37, 25, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338325243 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243 Building ZINC001338325243 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338325243 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 103) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(=O)N(C)CC(=O)N[C@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338325243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325243 none CC(=O)N(C)CC(=O)N[C@H]1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 50, 34, 34, 34, 23, 23, 23, 23, 23, 17, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 47, 47, 34, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 104) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(=O)N(C)CC(=O)N[C@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338325243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325243 none CC(=O)N(C)CC(=O)N[C@H]1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 37, 37, 37, 25, 25, 25, 25, 25, 17, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 49, 49, 37, 25, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338325243 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325243 Building ZINC001338325244 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338325244 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/105 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338325244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325244 none CC(=O)N(C)CC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 35, 35, 27, 27, 27, 27, 27, 15, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 35, 27, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 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: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/106 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338325244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325244 none CC(=O)N(C)CC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 50, 34, 34, 34, 25, 25, 25, 25, 25, 14, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 47, 47, 34, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338325244 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244 Building ZINC001338325244 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338325244 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 105) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(=O)N(C)CC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338325244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325244 none CC(=O)N(C)CC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 35, 35, 27, 27, 27, 27, 27, 15, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 35, 27, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 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: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 106) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(=O)N(C)CC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338325244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325244 none CC(=O)N(C)CC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 50, 34, 34, 34, 25, 25, 25, 25, 25, 14, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 47, 47, 34, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338325244 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325244 Building ZINC001338325245 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338325245 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/107 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338325245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325245 none CC(=O)N(C)CC(=O)N[C@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 40, 40, 40, 26, 26, 26, 26, 26, 10, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 49, 49, 40, 26, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/108 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338325245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325245 none CC(=O)N(C)CC(=O)N[C@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 42, 42, 42, 27, 27, 27, 27, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 49, 49, 42, 27, 27, 27, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338325245 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245 Building ZINC001338325245 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338325245 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 107) grep: /scratch/xiaobo/2379/xbv-8058097.48/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(=O)N(C)CC(=O)N[C@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338325245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325245 none CC(=O)N(C)CC(=O)N[C@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 40, 40, 40, 26, 26, 26, 26, 26, 10, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 49, 49, 40, 26, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 108) grep: /scratch/xiaobo/2379/xbv-8058097.48/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(=O)N(C)CC(=O)N[C@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338325245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338325245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338325245 none CC(=O)N(C)CC(=O)N[C@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 42, 42, 42, 27, 27, 27, 27, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 49, 49, 42, 27, 27, 27, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338325245 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338325245 Building ZINC001338332083 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338332083 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/109 `/scratch/xiaobo/2379/xbv-8058097.48/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)NC[C@@H]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338332083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332083 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 25, 25, 25, 25, 25, 25, 35, 35, 35, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 25, 25, 25, 25, 35, 50, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/110 `/scratch/xiaobo/2379/xbv-8058097.48/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)NC[C@@H]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338332083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332083 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 11, 23, 23, 23, 23, 23, 23, 34, 34, 34, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 34, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338332083 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083 Building ZINC001338332083 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338332083 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 109) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)NC[C@@H]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338332083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332083 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 25, 25, 25, 25, 25, 25, 35, 35, 35, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 25, 25, 25, 25, 35, 50, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 110) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)NC[C@@H]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338332083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332083 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 11, 23, 23, 23, 23, 23, 23, 34, 34, 34, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 34, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338332083 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332083 Building ZINC001338332084 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338332084 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/111 `/scratch/xiaobo/2379/xbv-8058097.48/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)NC[C@@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338332084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332084 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 13, 13, 13, 13, 13, 13, 23, 23, 23, 44, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 13, 13, 13, 13, 23, 44, 44, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/112 `/scratch/xiaobo/2379/xbv-8058097.48/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)NC[C@@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338332084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332084 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 15, 15, 15, 15, 15, 15, 23, 23, 23, 42, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 23, 42, 42, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338332084 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084 Building ZINC001338332084 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338332084 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 111) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)NC[C@@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338332084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332084 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 13, 13, 13, 13, 13, 13, 23, 23, 23, 44, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 13, 13, 13, 13, 23, 44, 44, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 112) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)NC[C@@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338332084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332084 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 15, 15, 15, 15, 15, 15, 23, 23, 23, 42, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 23, 42, 42, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338332084 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332084 Building ZINC001338332085 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338332085 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/113 `/scratch/xiaobo/2379/xbv-8058097.48/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)NC[C@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338332085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332085 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 23, 36, 36, 36, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 23, 23, 23, 23, 36, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/114 `/scratch/xiaobo/2379/xbv-8058097.48/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)NC[C@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338332085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332085 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 23, 23, 23, 23, 23, 23, 34, 34, 34, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 23, 23, 23, 23, 34, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338332085 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085 Building ZINC001338332085 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338332085 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 113) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)NC[C@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338332085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332085 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 23, 36, 36, 36, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 23, 23, 23, 23, 36, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 114) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)NC[C@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338332085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332085 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 23, 23, 23, 23, 23, 23, 34, 34, 34, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 23, 23, 23, 23, 34, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338332085 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332085 Building ZINC001338332086 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338332086 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/115 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338332086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332086 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 8, 15, 15, 15, 15, 15, 15, 23, 23, 23, 42, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 23, 42, 42, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/116 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338332086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332086 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 15, 15, 15, 15, 15, 15, 23, 23, 23, 43, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 23, 43, 43, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338332086 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086 Building ZINC001338332086 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338332086 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 115) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338332086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332086 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 8, 15, 15, 15, 15, 15, 15, 23, 23, 23, 42, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 23, 42, 42, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 116) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1) `ZINC001338332086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338332086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338332086 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 15, 15, 15, 15, 15, 15, 23, 23, 23, 43, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 23, 43, 43, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338332086 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338332086 Building ZINC001338343909 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338343909 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/117 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338343909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343909 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 21, 21, 21, 21, 30, 30, 30, 47, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 21, 21, 21, 21, 30, 47, 47, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/118 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338343909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343909 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 22, 22, 22, 22, 22, 22, 27, 27, 27, 46, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 22, 22, 22, 27, 46, 46, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338343909 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909 Building ZINC001338343909 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338343909 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 117) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338343909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343909 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 21, 21, 21, 21, 30, 30, 30, 47, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 21, 21, 21, 21, 30, 47, 47, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 118) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338343909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343909 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 22, 22, 22, 22, 22, 22, 27, 27, 27, 46, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 22, 22, 22, 27, 46, 46, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338343909 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343909 Building ZINC001338343910 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338343910 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/119 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338343910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343910 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 23, 23, 23, 23, 23, 23, 28, 28, 28, 45, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 28, 45, 45, 50, 50, 23, 23] 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: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/120 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338343910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343910 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 19, 19, 19, 28, 28, 28, 47, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 19, 19, 19, 19, 28, 47, 47, 50, 50, 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338343910 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910 Building ZINC001338343910 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338343910 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 119) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338343910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343910 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 23, 23, 23, 23, 23, 23, 28, 28, 28, 45, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 28, 45, 45, 50, 50, 23, 23] 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: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 120) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338343910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343910 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 19, 19, 19, 28, 28, 28, 47, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 19, 19, 19, 19, 28, 47, 47, 50, 50, 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338343910 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343910 Building ZINC001338343911 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338343911 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/121 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338343911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343911 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 24, 37, 37, 37, 48, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 24, 24, 24, 24, 37, 48, 48, 50, 50, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/122 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338343911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343911 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 24, 24, 24, 24, 24, 24, 33, 33, 33, 49, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 24, 24, 33, 49, 49, 50, 50, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338343911 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911 Building ZINC001338343911 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338343911 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 121) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338343911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343911 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 24, 37, 37, 37, 48, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 24, 24, 24, 24, 37, 48, 48, 50, 50, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 122) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338343911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343911 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 24, 24, 24, 24, 24, 24, 33, 33, 33, 49, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 24, 24, 33, 49, 49, 50, 50, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338343911 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343911 Building ZINC001338343912 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338343912 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/123 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338343912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343912 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 29, 29, 29, 29, 29, 29, 38, 38, 38, 50, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 38, 50, 50, 50, 50, 29, 29] 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: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/124 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338343912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343912 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 27, 27, 27, 27, 27, 27, 38, 38, 38, 49, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 27, 27, 27, 27, 38, 49, 49, 50, 50, 27, 27] 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/2379/xbv-8058097.48/working/building/ZINC001338343912 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338343912 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912 Building ZINC001338343912 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338343912 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 123) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338343912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343912 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 29, 29, 29, 29, 29, 29, 38, 38, 38, 50, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 38, 50, 50, 50, 50, 29, 29] 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: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 124) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1) `ZINC001338343912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338343912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338343912 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)Cc2cc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 27, 27, 27, 27, 27, 27, 38, 38, 38, 49, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 27, 27, 27, 27, 38, 49, 49, 50, 50, 27, 27] 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/2379/xbv-8058097.48/working/building/ZINC001338343912 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338343912 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338343912 Building ZINC001338344303 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344303 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/125 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344303 none CCn1nncc1C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 28, 26, 13, 13, 13, 13, 13, 6, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 34, 28, 26, 26, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/126 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344303 none CCn1nncc1C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 28, 25, 12, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 34, 28, 25, 25, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344303 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303 Building ZINC001338344303 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344303 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 125) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1nncc1C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344303 none CCn1nncc1C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 28, 26, 13, 13, 13, 13, 13, 6, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 34, 28, 26, 26, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 126) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1nncc1C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344303 none CCn1nncc1C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 28, 25, 12, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 34, 28, 25, 25, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344303 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344303 Building ZINC001338344305 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344305 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/127 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344305 none CCn1nncc1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 27, 14, 14, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 34, 30, 27, 27, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/128 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344305 none CCn1nncc1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 37, 30, 30, 30, 27, 12, 12, 12, 12, 12, 6, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 37, 30, 27, 27, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344305 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305 Building ZINC001338344305 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344305 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 127) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1nncc1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344305 none CCn1nncc1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 27, 14, 14, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 34, 30, 27, 27, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 128) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1nncc1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344305 none CCn1nncc1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 37, 30, 30, 30, 27, 12, 12, 12, 12, 12, 6, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 37, 30, 27, 27, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344305 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344305 Building ZINC001338344308 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344308 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/129 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344308 none CCn1nncc1C(=O)NC[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 40, 40, 39, 39, 39, 14, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 40, 39, 14, 14, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/130 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/130' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344308 none CCn1nncc1C(=O)NC[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 34, 13, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 34, 34, 13, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [49, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/2379/xbv-8058097.48/working/building/ZINC001338344308 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344308 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308 Building ZINC001338344308 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344308 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 129) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1nncc1C(=O)NC[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344308 none CCn1nncc1C(=O)NC[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 40, 40, 39, 39, 39, 14, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 40, 39, 14, 14, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 130) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1nncc1C(=O)NC[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344308 none CCn1nncc1C(=O)NC[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 34, 13, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 34, 34, 13, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [49, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/2379/xbv-8058097.48/working/building/ZINC001338344308 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344308 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344308 Building ZINC001338344311 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344311 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/131 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344311 none CCn1nncc1C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 37, 35, 35, 35, 14, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 37, 35, 14, 14, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/132 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/132' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344311 none CCn1nncc1C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 37, 37, 37, 18, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 39, 37, 18, 18, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344311 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311 Building ZINC001338344311 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344311 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 131) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1nncc1C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344311 none CCn1nncc1C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 37, 35, 35, 35, 14, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 37, 35, 14, 14, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 132) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1nncc1C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338344311 none CCn1nncc1C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 37, 37, 37, 18, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 39, 37, 18, 18, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344311 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344311 Building ZINC001338344520 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344520 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/133 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344520 none CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 50, 24, 24, 24, 21, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 36, 36, 24, 21, 21, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 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: 200 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/134 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/134' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344520 none CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 50, 26, 26, 26, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 39, 39, 26, 18, 18, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 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: 192 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344520 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520 Building ZINC001338344520 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344520 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 133) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344520 none CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 50, 24, 24, 24, 21, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 36, 36, 24, 21, 21, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 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: 200 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 134) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344520 none CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 50, 26, 26, 26, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 39, 39, 26, 18, 18, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 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: 192 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344520 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344520 Building ZINC001338344521 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344521 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/135 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344521 none CN(C)C(=O)CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 50, 26, 26, 26, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 38, 38, 26, 18, 18, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 190 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/136 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/136' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344521 none CN(C)C(=O)CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 50, 22, 22, 22, 17, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 37, 37, 22, 17, 17, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 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: 199 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344521 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521 Building ZINC001338344521 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344521 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 135) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)C(=O)CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344521 none CN(C)C(=O)CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 50, 26, 26, 26, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 38, 38, 26, 18, 18, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 190 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 136) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)C(=O)CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344521 none CN(C)C(=O)CC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 50, 22, 22, 22, 17, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 37, 37, 22, 17, 17, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 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: 199 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344521 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344521 Building ZINC001338344522 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344522 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/137 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)NC[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344522 none CN(C)C(=O)CC(=O)NC[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 50, 34, 34, 34, 9, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 48, 48, 34, 9, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52]) total number of confs: 180 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/138 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)NC[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344522 none CN(C)C(=O)CC(=O)NC[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 50, 38, 38, 38, 11, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 47, 47, 38, 11, 11, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344522 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522 Building ZINC001338344522 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344522 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 137) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)C(=O)CC(=O)NC[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344522 none CN(C)C(=O)CC(=O)NC[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 50, 34, 34, 34, 9, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 48, 48, 34, 9, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52]) total number of confs: 180 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 138) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)C(=O)CC(=O)NC[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344522 none CN(C)C(=O)CC(=O)NC[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 50, 38, 38, 38, 11, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 47, 47, 38, 11, 11, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344522 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344522 Building ZINC001338344523 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344523 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/139 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344523 none CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 50, 42, 42, 42, 17, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 48, 48, 42, 17, 17, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/140 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/140' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344523 none CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 40, 40, 40, 14, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 49, 49, 40, 14, 14, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 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: 182 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344523 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523 Building ZINC001338344523 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338344523 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 139) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)C(=O)CC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338344523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344523 none CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 50, 42, 42, 42, 17, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 48, 48, 42, 17, 17, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 140) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)C(=O)CC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338344523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338344523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338344523 none CN(C)C(=O)CC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 40, 40, 40, 14, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 49, 49, 40, 14, 14, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 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: 182 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338344523 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338344523 Building ZINC001338346990 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338346990 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/141 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338346990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346990 none Cn1cc(CC(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 37, 22, 22, 22, 16, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 37, 37, 22, 16, 16, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/142 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338346990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346990 none Cn1cc(CC(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 17, 17, 17, 14, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 33, 33, 17, 14, 14, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338346990 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990 Building ZINC001338346990 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338346990 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 141) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338346990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346990 none Cn1cc(CC(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 37, 22, 22, 22, 16, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 37, 37, 22, 16, 16, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 142) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338346990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346990 none Cn1cc(CC(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 17, 17, 17, 14, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 33, 33, 17, 14, 14, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338346990 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346990 Building ZINC001338346993 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338346993 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/143 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)NC[C@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338346993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346993 none Cn1cc(CC(=O)NC[C@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 26, 26, 26, 10, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 48, 48, 26, 10, 10, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/144 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)NC[C@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338346993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346993 none Cn1cc(CC(=O)NC[C@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 28, 28, 28, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 47, 47, 28, 12, 12, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338346993 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993 Building ZINC001338346993 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338346993 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 143) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(CC(=O)NC[C@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338346993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346993 none Cn1cc(CC(=O)NC[C@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 26, 26, 26, 10, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 48, 48, 26, 10, 10, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 144) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(CC(=O)NC[C@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338346993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346993 none Cn1cc(CC(=O)NC[C@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 28, 28, 28, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 47, 47, 28, 12, 12, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338346993 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346993 Building ZINC001338346996 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338346996 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/145 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)NC[C@@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338346996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346996 none Cn1cc(CC(=O)NC[C@@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 34, 18, 18, 18, 15, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 34, 34, 18, 15, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/146 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/146' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)NC[C@@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338346996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346996 none Cn1cc(CC(=O)NC[C@@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 35, 20, 20, 20, 15, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 35, 35, 20, 15, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338346996 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996 Building ZINC001338346996 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338346996 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 145) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)NC[C@@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338346996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346996 none Cn1cc(CC(=O)NC[C@@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 34, 18, 18, 18, 15, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 34, 34, 18, 15, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 146) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)NC[C@@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338346996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346996 none Cn1cc(CC(=O)NC[C@@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 35, 20, 20, 20, 15, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 35, 35, 20, 15, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338346996 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346996 Building ZINC001338346999 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338346999 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/147 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)NC[C@@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338346999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346999 none Cn1cc(CC(=O)NC[C@@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 34, 34, 34, 16, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 44, 44, 34, 16, 16, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/148 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/148' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)NC[C@@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338346999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346999 none Cn1cc(CC(=O)NC[C@@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 37, 37, 37, 14, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 46, 46, 37, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50] 50 rigid atoms, others: [48, 45, 49, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338346999 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999 Building ZINC001338346999 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338346999 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 147) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(CC(=O)NC[C@@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338346999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346999 none Cn1cc(CC(=O)NC[C@@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 34, 34, 34, 16, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 44, 44, 34, 16, 16, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 148) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(CC(=O)NC[C@@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001338346999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338346999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338346999 none Cn1cc(CC(=O)NC[C@@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 37, 37, 37, 14, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 46, 46, 37, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50] 50 rigid atoms, others: [48, 45, 49, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338346999 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338346999 Building ZINC001338347882 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338347882 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/149 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338347882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338347882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338347882 none COCCOCC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 47, 31, 31, 31, 14, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 49, 49, 47, 47, 31, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/150 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338347882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338347882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338347882 none COCCOCC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 42, 38, 27, 27, 27, 8, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 44, 44, 38, 38, 27, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338347882 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882 Building ZINC001338347882 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338347882 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 149) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338347882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338347882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338347882 none COCCOCC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 47, 31, 31, 31, 14, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 49, 49, 47, 47, 31, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 150) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338347882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338347882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338347882 none COCCOCC(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 42, 38, 27, 27, 27, 8, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 44, 44, 38, 38, 27, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338347882 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347882 Building ZINC001338347883 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338347883 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/151 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338347883.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338347883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338347883 none COCCOCC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 20, 20, 20, 16, 8, 8, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 43, 43, 20, 16, 16, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/152 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/152' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338347883.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338347883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338347883 none COCCOCC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 46, 21, 21, 21, 17, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 49, 49, 46, 46, 21, 17, 17, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338347883 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883 Building ZINC001338347883 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338347883 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 151) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338347883.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338347883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338347883 none COCCOCC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 20, 20, 20, 16, 8, 8, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 43, 43, 20, 16, 16, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 152) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338347883.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338347883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338347883 none COCCOCC(=O)NC[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 46, 21, 21, 21, 17, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 49, 49, 46, 46, 21, 17, 17, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338347883 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347883 Building ZINC001338347884 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338347884 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/153 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338347884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338347884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338347884 none COCCOCC(=O)NC[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 42, 40, 25, 25, 25, 9, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 44, 44, 40, 40, 25, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/154 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338347884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338347884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338347884 none COCCOCC(=O)NC[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 46, 43, 23, 23, 23, 10, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 46, 46, 43, 43, 23, 10, 10, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338347884 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884 Building ZINC001338347884 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338347884 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 153) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)NC[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338347884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338347884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338347884 none COCCOCC(=O)NC[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 42, 40, 25, 25, 25, 9, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 44, 44, 40, 40, 25, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 154) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)NC[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338347884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338347884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338347884 none COCCOCC(=O)NC[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 46, 43, 23, 23, 23, 10, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 46, 46, 43, 43, 23, 10, 10, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338347884 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338347884 Building ZINC001338352401 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338352401 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/155 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001338352401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338352401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338352401 none Cn1cc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 47, 47, 29, 29, 29, 29, 29, 13, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 47, 29, 29, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/156 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001338352401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338352401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338352401 none Cn1cc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 47, 47, 28, 28, 28, 28, 28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 47, 28, 28, 28, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338352401 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401 Building ZINC001338352401 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338352401 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 155) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001338352401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338352401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338352401 none Cn1cc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 47, 47, 29, 29, 29, 29, 29, 13, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 47, 29, 29, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 156) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001338352401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338352401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338352401 none Cn1cc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 47, 47, 28, 28, 28, 28, 28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 47, 28, 28, 28, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338352401 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352401 Building ZINC001338352402 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338352402 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/157 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001338352402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338352402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338352402 none Cn1cc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 48, 48, 33, 33, 33, 33, 33, 20, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 48, 33, 33, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/158 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001338352402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338352402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338352402 none Cn1cc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 49, 31, 31, 31, 31, 30, 19, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 49, 31, 31, 31, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338352402 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402 Building ZINC001338352402 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338352402 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 157) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001338352402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338352402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338352402 none Cn1cc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 48, 48, 33, 33, 33, 33, 33, 20, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 48, 33, 33, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 158) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001338352402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338352402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338352402 none Cn1cc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 49, 31, 31, 31, 31, 30, 19, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 49, 31, 31, 31, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338352402 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352402 Building ZINC001338352403 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338352403 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/159 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001338352403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338352403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338352403 none Cn1cc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 45, 45, 28, 28, 28, 28, 28, 16, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 45, 28, 28, 28, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/160 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/160' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001338352403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338352403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338352403 none Cn1cc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 47, 47, 31, 31, 31, 31, 31, 16, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 47, 31, 31, 31, 31, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338352403 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403 Building ZINC001338352403 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338352403 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 159) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001338352403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338352403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338352403 none Cn1cc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 45, 45, 28, 28, 28, 28, 28, 16, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 45, 28, 28, 28, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 160) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001338352403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338352403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338352403 none Cn1cc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 47, 47, 31, 31, 31, 31, 31, 16, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 47, 31, 31, 31, 31, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338352403 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338352403 Building ZINC001338369534 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338369534 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/161 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CCN(C(=O)CC(F)(F)F)CC2)cn1) `ZINC001338369534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338369534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338369534 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CCN(C(=O)CC(F)(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 28, 28, 40, 40, 40, 40, 12, 12, 6, 6, 6, 6, 6, 6, 3, 12, 12, 12, 12, 12, 40, 40, 12, 12, 12, 12, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 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]) total number of confs: 144 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/162 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/162' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2CCN(C(=O)CC(F)(F)F)CC2)cn1) `ZINC001338369534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338369534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338369534 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2CCN(C(=O)CC(F)(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 28, 28, 41, 41, 41, 41, 13, 13, 6, 6, 6, 6, 6, 6, 3, 13, 13, 13, 13, 13, 41, 41, 13, 13, 13, 13, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 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]) total number of confs: 150 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338369534 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534 Building ZINC001338369534 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338369534 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 161) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CCN(C(=O)CC(F)(F)F)CC2)cn1) `ZINC001338369534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338369534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338369534 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CCN(C(=O)CC(F)(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 28, 28, 40, 40, 40, 40, 12, 12, 6, 6, 6, 6, 6, 6, 3, 12, 12, 12, 12, 12, 40, 40, 12, 12, 12, 12, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 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]) total number of confs: 144 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 162) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2CCN(C(=O)CC(F)(F)F)CC2)cn1) `ZINC001338369534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338369534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338369534 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2CCN(C(=O)CC(F)(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 28, 28, 41, 41, 41, 41, 13, 13, 6, 6, 6, 6, 6, 6, 3, 13, 13, 13, 13, 13, 41, 41, 13, 13, 13, 13, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 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]) total number of confs: 150 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338369534 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338369534 Building ZINC001338375618 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338375618 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/163 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338375618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375618 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 14, 14, 14, 14, 14, 14, 20, 20, 20, 37, 39, 49, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 14, 14, 20, 37, 37, 42, 42, 48, 48, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/164 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338375618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375618 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 11, 11, 11, 11, 15, 15, 15, 28, 36, 48, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 15, 28, 28, 40, 40, 45, 46, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 231 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338375618 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618 Building ZINC001338375618 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338375618 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 163) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338375618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375618 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 14, 14, 14, 14, 14, 14, 20, 20, 20, 37, 39, 49, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 14, 14, 20, 37, 37, 42, 42, 48, 48, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 164) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338375618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375618 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 11, 11, 11, 11, 15, 15, 15, 28, 36, 48, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 15, 28, 28, 40, 40, 45, 46, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 231 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338375618 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375618 Building ZINC001338375620 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338375620 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/165 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338375620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375620 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 15, 15, 15, 28, 36, 48, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 15, 28, 28, 40, 40, 46, 45, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/166 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338375620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375620 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 19, 19, 19, 36, 39, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 13, 13, 13, 19, 36, 36, 43, 43, 48, 49, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338375620 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620 Building ZINC001338375620 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338375620 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 165) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338375620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375620 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 15, 15, 15, 28, 36, 48, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 15, 28, 28, 40, 40, 46, 45, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 166) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338375620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375620 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 19, 19, 19, 36, 39, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 13, 13, 13, 19, 36, 36, 43, 43, 48, 49, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338375620 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375620 Building ZINC001338375622 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338375622 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/167 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338375622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375622 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 21, 21, 21, 39, 32, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 17, 17, 17, 17, 21, 39, 39, 43, 43, 45, 44, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/168 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338375622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375622 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 17, 17, 17, 17, 26, 26, 26, 45, 35, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 17, 17, 17, 26, 45, 45, 46, 46, 47, 43, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338375622 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622 Building ZINC001338375622 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338375622 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 167) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338375622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375622 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 21, 21, 21, 39, 32, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 17, 17, 17, 17, 21, 39, 39, 43, 43, 45, 44, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 168) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338375622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375622 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 17, 17, 17, 17, 26, 26, 26, 45, 35, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 17, 17, 17, 26, 45, 45, 46, 46, 47, 43, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338375622 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375622 Building ZINC001338375624 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338375624 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/169 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338375624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375624 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 18, 18, 18, 18, 26, 26, 26, 45, 36, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 18, 18, 26, 45, 45, 46, 46, 42, 48, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/170 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338375624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375624 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 25, 25, 25, 42, 37, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 16, 16, 16, 16, 25, 42, 42, 46, 46, 45, 45, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338375624 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624 Building ZINC001338375624 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338375624 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 169) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338375624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375624 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 18, 18, 18, 18, 26, 26, 26, 45, 36, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 18, 18, 26, 45, 45, 46, 46, 42, 48, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 170) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1) `ZINC001338375624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338375624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338375624 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 25, 25, 25, 42, 37, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 16, 16, 16, 16, 25, 42, 42, 46, 46, 45, 45, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338375624 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338375624 Building ZINC001338387014 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338387014 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/171 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338387014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387014 none Cn1ncc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 14, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36] 50 rigid atoms, others: [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: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/172 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338387014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387014 none Cn1ncc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 18, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 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: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338387014 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014 Building ZINC001338387014 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338387014 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 171) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1ncc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338387014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387014 none Cn1ncc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 14, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36] 50 rigid atoms, others: [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: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 172) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1ncc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338387014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387014 none Cn1ncc(C(=O)N[C@@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 18, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 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: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338387014 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387014 Building ZINC001338387015 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338387015 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/173 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338387015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387015 none Cn1ncc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 49, 49, 39, 39, 39, 39, 39, 20, 39, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 49, 39, 39, 39, 39, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39] 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: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/174 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338387015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387015 none Cn1ncc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 43, 43, 20, 43, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 50, 50, 50, 43, 43, 43, 43, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43] 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: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338387015 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015 Building ZINC001338387015 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338387015 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 173) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1ncc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338387015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387015 none Cn1ncc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 49, 49, 39, 39, 39, 39, 39, 20, 39, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 49, 39, 39, 39, 39, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39] 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: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 174) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1ncc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338387015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387015 none Cn1ncc(C(=O)N[C@H]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 43, 43, 20, 43, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 50, 50, 50, 43, 43, 43, 43, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43] 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: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338387015 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387015 Building ZINC001338387016 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338387016 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/175 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338387016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387016 none Cn1ncc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 17, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 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: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/176 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338387016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387016 none Cn1ncc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 20, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36] 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: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338387016 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016 Building ZINC001338387016 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338387016 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 175) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1ncc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338387016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387016 none Cn1ncc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 17, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 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: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 176) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1ncc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338387016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387016 none Cn1ncc(C(=O)N[C@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 20, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36] 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: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338387016 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387016 Building ZINC001338387017 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338387017 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/177 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338387017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387017 none Cn1ncc(C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 15, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36] 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: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/178 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338387017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387017 none Cn1ncc(C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40] 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338387017 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017 Building ZINC001338387017 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338387017 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 177) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1ncc(C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338387017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387017 none Cn1ncc(C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 15, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36] 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: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 178) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1ncc(C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001338387017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338387017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338387017 none Cn1ncc(C(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40] 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338387017 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338387017 Building ZINC001338388597 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338388597 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/179 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)NC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1=O) `ZINC001338388597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338388597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338388597 none CC1(C)NC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 29, 17, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 19, 19, 10, 10, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/180 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/180' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)NC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1=O) `ZINC001338388597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338388597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338388597 none CC1(C)NC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 29, 18, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 20, 20, 10, 10, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338388597 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597 Building ZINC001338388597 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338388597 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 179) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC1(C)NC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1=O) `ZINC001338388597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338388597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338388597 none CC1(C)NC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 29, 17, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 19, 19, 10, 10, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 180) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC1(C)NC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1=O) `ZINC001338388597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338388597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338388597 none CC1(C)NC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 29, 18, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 20, 20, 10, 10, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338388597 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338388597 Building ZINC001338392776 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338392776 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/181 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338392776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392776 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 17, 28, 28, 28, 43, 50, 50, 43, 43, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 17, 17, 17, 28, 50, 50, 43, 43, 43, 43, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/182 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338392776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392776 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total 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, 8, 21, 21, 21, 21, 21, 21, 26, 26, 26, 43, 50, 50, 43, 43, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 26, 50, 50, 43, 43, 43, 43, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338392776 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776 Building ZINC001338392776 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338392776 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 181) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338392776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392776 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 17, 28, 28, 28, 43, 50, 50, 43, 43, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 17, 17, 17, 28, 50, 50, 43, 43, 43, 43, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 182) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338392776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392776 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total 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, 8, 21, 21, 21, 21, 21, 21, 26, 26, 26, 43, 50, 50, 43, 43, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 26, 50, 50, 43, 43, 43, 43, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338392776 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392776 Building ZINC001338392781 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338392781 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/183 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338392781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392781 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total 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, 15, 24, 24, 24, 24, 24, 24, 35, 35, 35, 46, 50, 50, 46, 46, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 24, 24, 24, 24, 35, 50, 50, 46, 46, 46, 46, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/184 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338392781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392781 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 21, 21, 21, 21, 35, 35, 35, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 21, 21, 21, 35, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338392781 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781 Building ZINC001338392781 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338392781 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 183) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338392781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392781 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total 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, 15, 24, 24, 24, 24, 24, 24, 35, 35, 35, 46, 50, 50, 46, 46, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 24, 24, 24, 24, 35, 50, 50, 46, 46, 46, 46, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 184) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338392781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392781 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 21, 21, 21, 21, 35, 35, 35, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 21, 21, 21, 35, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338392781 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392781 Building ZINC001338392784 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338392784 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/185 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338392784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392784 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 21, 21, 21, 21, 30, 30, 30, 45, 50, 50, 45, 45, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 21, 21, 21, 21, 30, 50, 50, 45, 45, 45, 45, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/186 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338392784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392784 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total 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, 17, 17, 17, 17, 17, 17, 27, 27, 27, 42, 50, 50, 42, 42, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 27, 50, 50, 42, 42, 42, 42, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338392784 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784 Building ZINC001338392784 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338392784 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 185) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338392784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392784 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 21, 21, 21, 21, 30, 30, 30, 45, 50, 50, 45, 45, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 21, 21, 21, 21, 30, 50, 50, 45, 45, 45, 45, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 186) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338392784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392784 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total 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, 17, 17, 17, 17, 17, 17, 27, 27, 27, 42, 50, 50, 42, 42, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 27, 50, 50, 42, 42, 42, 42, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338392784 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392784 Building ZINC001338392787 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338392787 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/187 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338392787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392787 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 20, 20, 20, 20, 20, 20, 36, 36, 36, 48, 50, 50, 48, 48, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 20, 20, 20, 20, 36, 50, 50, 48, 48, 48, 48, 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: 164 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/188 `/scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338392787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392787 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 24, 36, 36, 36, 47, 50, 50, 47, 47, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 24, 24, 24, 36, 50, 50, 47, 47, 47, 47, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338392787 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787 Building ZINC001338392787 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338392787 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 187) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338392787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392787 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 20, 20, 20, 20, 20, 20, 36, 36, 36, 48, 50, 50, 48, 48, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 20, 20, 20, 20, 36, 50, 50, 48, 48, 48, 48, 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: 164 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 188) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1) `ZINC001338392787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338392787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338392787 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)C2(C(N)=O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 24, 36, 36, 36, 47, 50, 50, 47, 47, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 24, 24, 24, 36, 50, 50, 47, 47, 47, 47, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338392787 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338392787 Building ZINC001338394927 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338394927 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/189 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338394927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394927 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 21, 21, 21, 21, 31, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/190 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338394927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394927 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 25, 25, 25, 25, 29, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338394927 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927 Building ZINC001338394927 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338394927 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 189) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338394927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394927 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 21, 21, 21, 21, 31, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 190) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338394927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394927 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 25, 25, 25, 25, 29, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338394927 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394927 Building ZINC001338394928 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338394928 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/191 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338394928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394928 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 22, 22, 22, 22, 22, 22, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 22, 22, 22, 28, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/192 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338394928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394928 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 25, 25, 25, 25, 25, 25, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 25, 25, 25, 25, 35, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338394928 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928 Building ZINC001338394928 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338394928 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 191) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338394928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394928 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 22, 22, 22, 22, 22, 22, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 22, 22, 22, 28, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 192) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338394928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394928 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 25, 25, 25, 25, 25, 25, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 25, 25, 25, 25, 35, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338394928 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394928 Building ZINC001338394929 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338394929 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/193 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338394929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394929 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 22, 22, 22, 22, 22, 22, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 22, 22, 22, 22, 27, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/194 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/194' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338394929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394929 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 23, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 27, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338394929 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929 Building ZINC001338394929 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338394929 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 193) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338394929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394929 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 22, 22, 22, 22, 22, 22, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 22, 22, 22, 22, 27, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 194) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338394929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394929 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 23, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 27, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338394929 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394929 Building ZINC001338394930 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338394930 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/195 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338394930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394930 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 22, 22, 22, 22, 22, 22, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 22, 22, 22, 22, 26, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/196 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/196' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338394930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394930 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 20, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 20, 20, 20, 25, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338394930 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930 Building ZINC001338394930 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338394930 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 195) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338394930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394930 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 22, 22, 22, 22, 22, 22, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 22, 22, 22, 22, 26, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 196) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1) `ZINC001338394930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338394930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001338394930 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 20, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 20, 20, 20, 25, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338394930 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338394930 Building ZINC001338411674 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338411674 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/197 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)COc3ccccc32)cn1) `ZINC001338411674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338411674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338411674 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)COc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 21, 32, 32, 32, 32, 32, 32, 32, 32, 32, 27, 6, 6, 6, 6, 6, 6, 2, 15, 15, 21, 21, 32, 32, 32, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 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]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/198 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/198' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)COc3ccccc32)cn1) `ZINC001338411674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338411674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338411674 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)COc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 29, 6, 6, 6, 6, 6, 6, 3, 17, 17, 23, 23, 34, 34, 34, 34, 34, 34, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 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]) total number of confs: 119 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338411674 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674 Building ZINC001338411674 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338411674 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 197) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)COc3ccccc32)cn1) `ZINC001338411674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338411674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338411674 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)COc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 21, 32, 32, 32, 32, 32, 32, 32, 32, 32, 27, 6, 6, 6, 6, 6, 6, 2, 15, 15, 21, 21, 32, 32, 32, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 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]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 198) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)COc3ccccc32)cn1) `ZINC001338411674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338411674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001338411674 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)COc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 29, 6, 6, 6, 6, 6, 6, 3, 17, 17, 23, 23, 34, 34, 34, 34, 34, 34, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 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]) total number of confs: 119 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338411674 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338411674 Building ZINC001338422414 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338422414 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/199 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1) `ZINC001338422414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338422414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001338422414 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 14, 9, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 33, 33, 50, 50, 50, 50, 24, 24, 24, 14, 14, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/200 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/200' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1) `ZINC001338422414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338422414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001338422414 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 14, 9, 7, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 30, 30, 50, 50, 50, 50, 22, 22, 22, 14, 14, 27, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338422414 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414 Building ZINC001338422414 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338422414 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 199) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1) `ZINC001338422414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338422414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001338422414 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 14, 9, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 33, 33, 50, 50, 50, 50, 24, 24, 24, 14, 14, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 200) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1) `ZINC001338422414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338422414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001338422414 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 14, 9, 7, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 30, 30, 50, 50, 50, 50, 22, 22, 22, 14, 14, 27, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338422414 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422414 Building ZINC001338422417 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338422417 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/201 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1) `ZINC001338422417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338422417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001338422417 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 14, 9, 7, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 30, 30, 50, 50, 50, 50, 22, 22, 22, 14, 14, 27, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/202 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1) `ZINC001338422417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338422417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001338422417 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 15, 10, 6, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 32, 32, 50, 50, 50, 50, 25, 25, 25, 15, 15, 30, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 195 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338422417 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417 Building ZINC001338422417 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338422417 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 201) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1) `ZINC001338422417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338422417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001338422417 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 14, 9, 7, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 30, 30, 50, 50, 50, 50, 22, 22, 22, 14, 14, 27, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 202) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1) `ZINC001338422417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338422417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001338422417 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccsc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 15, 10, 6, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 32, 32, 50, 50, 50, 50, 25, 25, 25, 15, 15, 30, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 195 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338422417 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338422417 Building ZINC001338433446 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338433446 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/203 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1) `ZINC001338433446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338433446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338433446 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 11, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 32, 32, 50, 50, 50, 50, 50, 50, 20, 20, 20, 14, 14, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 187 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/204 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1) `ZINC001338433446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338433446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338433446 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 13, 9, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 36, 36, 50, 50, 50, 50, 50, 50, 23, 23, 23, 13, 13, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 192 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338433446 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446 Building ZINC001338433446 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338433446 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 203) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1) `ZINC001338433446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338433446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338433446 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 11, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 32, 32, 50, 50, 50, 50, 50, 50, 20, 20, 20, 14, 14, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 187 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 204) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1) `ZINC001338433446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338433446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338433446 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 13, 9, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 36, 36, 50, 50, 50, 50, 50, 50, 23, 23, 23, 13, 13, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 192 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338433446 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433446 Building ZINC001338433447 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338433447 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/205 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1) `ZINC001338433447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338433447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338433447 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 13, 9, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 36, 36, 50, 50, 50, 50, 50, 50, 23, 23, 23, 13, 13, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 192 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/206 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1) `ZINC001338433447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338433447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338433447 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 11, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 50, 50, 50, 50, 50, 50, 20, 20, 20, 14, 14, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 188 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338433447 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447 Building ZINC001338433447 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338433447 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 205) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1) `ZINC001338433447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338433447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338433447 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 13, 9, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 36, 36, 50, 50, 50, 50, 50, 50, 23, 23, 23, 13, 13, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 192 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 206) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1) `ZINC001338433447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338433447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338433447 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(Cl)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 11, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 50, 50, 50, 50, 50, 50, 20, 20, 20, 14, 14, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 188 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338433447 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338433447 Building ZINC001338434612 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338434612 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/207 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1) `ZINC001338434612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338434612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434612 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 22, 14, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 40, 43, 50, 50, 50, 50, 50, 26, 26, 26, 22, 22, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 43, 43, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 257 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/208 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1) `ZINC001338434612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338434612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434612 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 19, 14, 7, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 37, 37, 37, 41, 50, 50, 50, 50, 50, 22, 22, 22, 19, 19, 42, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 39, 39, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 246 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338434612 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612 Building ZINC001338434612 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338434612 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 207) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1) `ZINC001338434612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338434612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434612 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 22, 14, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 40, 43, 50, 50, 50, 50, 50, 26, 26, 26, 22, 22, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 43, 43, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 257 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 208) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1) `ZINC001338434612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338434612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434612 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 19, 14, 7, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 37, 37, 37, 41, 50, 50, 50, 50, 50, 22, 22, 22, 19, 19, 42, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 39, 39, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 246 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338434612 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434612 Building ZINC001338434613 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338434613 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/209 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1) `ZINC001338434613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338434613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434613 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 21, 14, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 38, 38, 40, 42, 50, 50, 50, 50, 50, 24, 24, 24, 21, 21, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 42, 42, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 248 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/210 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1) `ZINC001338434613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338434613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434613 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 17, 8, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 37, 37, 38, 40, 50, 50, 50, 50, 50, 23, 23, 23, 19, 19, 51, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 39, 39, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 242 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338434613 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613 Building ZINC001338434613 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338434613 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 209) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1) `ZINC001338434613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338434613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434613 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 21, 14, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 38, 38, 40, 42, 50, 50, 50, 50, 50, 24, 24, 24, 21, 21, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 42, 42, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 248 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 210) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1) `ZINC001338434613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338434613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434613 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 17, 8, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 37, 37, 38, 40, 50, 50, 50, 50, 50, 23, 23, 23, 19, 19, 51, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 39, 39, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 242 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338434613 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434613 Building ZINC001338434614 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338434614 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/211 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1) `ZINC001338434614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338434614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434614 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 17, 8, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 37, 37, 38, 40, 50, 50, 50, 50, 50, 23, 23, 23, 19, 19, 51, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 39, 39, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 242 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/212 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/212' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1) `ZINC001338434614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338434614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434614 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 21, 13, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 38, 38, 40, 42, 50, 50, 50, 50, 50, 24, 24, 24, 21, 21, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 42, 42, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 248 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338434614 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614 Building ZINC001338434614 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338434614 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 211) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1) `ZINC001338434614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338434614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434614 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 17, 8, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 37, 37, 38, 40, 50, 50, 50, 50, 50, 23, 23, 23, 19, 19, 51, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 39, 39, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 242 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 212) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1) `ZINC001338434614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338434614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434614 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 21, 13, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 38, 38, 40, 42, 50, 50, 50, 50, 50, 24, 24, 24, 21, 21, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 42, 42, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 248 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338434614 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434614 Building ZINC001338434615 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338434615 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/213 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1) `ZINC001338434615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338434615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434615 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 20, 14, 7, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 37, 37, 37, 41, 50, 50, 50, 50, 50, 22, 22, 22, 20, 20, 42, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 39, 39, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 248 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/214 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1) `ZINC001338434615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338434615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434615 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 22, 14, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 40, 43, 50, 50, 50, 50, 50, 26, 26, 26, 22, 22, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 43, 43, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 257 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338434615 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615 Building ZINC001338434615 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338434615 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 213) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1) `ZINC001338434615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338434615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434615 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 20, 14, 7, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 37, 37, 37, 41, 50, 50, 50, 50, 50, 22, 22, 22, 20, 20, 42, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 39, 39, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 248 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 214) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1) `ZINC001338434615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338434615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434615 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 22, 14, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 40, 43, 50, 50, 50, 50, 50, 26, 26, 26, 22, 22, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 43, 43, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 257 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338434615 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434615 Building ZINC001338434888 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338434888 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/215 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1) `ZINC001338434888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338434888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434888 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 12, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 23, 46, 50, 50, 50, 50, 13, 13, 13, 13, 13, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 210 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/216 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1) `ZINC001338434888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338434888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434888 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 14, 7, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 24, 44, 50, 50, 50, 50, 16, 16, 16, 16, 16, 42, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338434888 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888 Building ZINC001338434888 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338434888 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 215) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1) `ZINC001338434888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338434888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434888 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 12, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 23, 46, 50, 50, 50, 50, 13, 13, 13, 13, 13, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 210 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 216) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1) `ZINC001338434888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338434888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434888 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 14, 7, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 24, 44, 50, 50, 50, 50, 16, 16, 16, 16, 16, 42, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338434888 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434888 Building ZINC001338434889 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338434889 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/217 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1) `ZINC001338434889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338434889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434889 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 16, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 26, 46, 50, 50, 50, 50, 17, 17, 17, 17, 17, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/218 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1) `ZINC001338434889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338434889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434889 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 12, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 24, 45, 50, 50, 50, 50, 14, 14, 14, 14, 14, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338434889 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889 Building ZINC001338434889 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338434889 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 217) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1) `ZINC001338434889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338434889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434889 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 16, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 26, 46, 50, 50, 50, 50, 17, 17, 17, 17, 17, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 218) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1) `ZINC001338434889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338434889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338434889 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)COC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 12, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 24, 45, 50, 50, 50, 50, 14, 14, 14, 14, 14, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338434889 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338434889 Building ZINC001338449603 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338449603 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/219 `/scratch/xiaobo/2379/xbv-8058097.48/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)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338449603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338449603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338449603 none CCc1nc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need 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, 33, 33, 33, 19, 11, 8, 11, 11, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 50, 50, 50, 33, 19, 19, 33, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 266 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/220 `/scratch/xiaobo/2379/xbv-8058097.48/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)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338449603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338449603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338449603 none CCc1nc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)co1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 32, 32, 32, 32, 32, 32, 19, 10, 6, 10, 10, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50, 32, 19, 19, 30, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 280 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338449603 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603 Building ZINC001338449603 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338449603 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 219) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338449603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338449603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338449603 none CCc1nc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need 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, 33, 33, 33, 19, 11, 8, 11, 11, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 50, 50, 50, 33, 19, 19, 33, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 266 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 220) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338449603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338449603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338449603 none CCc1nc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)co1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 32, 32, 32, 32, 32, 32, 19, 10, 6, 10, 10, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50, 32, 19, 19, 30, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 280 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338449603 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449603 Building ZINC001338449604 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338449604 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/221 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338449604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338449604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338449604 none CCc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need 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, 35, 19, 10, 6, 10, 10, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 35, 19, 19, 30, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 268 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/222 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338449604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338449604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338449604 none CCc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)co1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need 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, 34, 34, 34, 20, 12, 8, 12, 12, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 34, 20, 20, 36, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 266 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338449604 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604 Building ZINC001338449604 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338449604 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 221) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338449604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338449604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338449604 none CCc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need 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, 35, 19, 10, 6, 10, 10, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 35, 19, 19, 30, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 268 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 222) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338449604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338449604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338449604 none CCc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)co1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need 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, 34, 34, 34, 20, 12, 8, 12, 12, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 34, 20, 20, 36, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 266 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338449604 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338449604 Building ZINC001338450235 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338450235 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/223 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338450235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338450235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338450235 none CN(C[C@@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 5, 6, 6, 6, 26, 45, 45, 45, 45, 45, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 5, 5, 6, 26, 26, 45, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/224 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338450235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338450235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338450235 none CN(C[C@@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 38, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 3, 3, 7, 38, 38, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 189 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338450235 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235 Building ZINC001338450235 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338450235 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 223) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338450235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338450235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338450235 none CN(C[C@@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 5, 6, 6, 6, 26, 45, 45, 45, 45, 45, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 5, 5, 6, 26, 26, 45, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 224) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338450235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338450235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338450235 none CN(C[C@@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 38, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 3, 3, 7, 38, 38, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 189 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338450235 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450235 Building ZINC001338450236 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338450236 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/225 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338450236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338450236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338450236 none CN(C[C@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 36, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 3, 3, 7, 36, 36, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/226 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338450236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338450236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338450236 none CN(C[C@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 6, 7, 7, 7, 27, 46, 46, 46, 46, 46, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 6, 6, 7, 27, 27, 46, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338450236 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236 Building ZINC001338450236 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338450236 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 225) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338450236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338450236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338450236 none CN(C[C@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 36, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 3, 3, 7, 36, 36, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 226) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338450236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338450236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338450236 none CN(C[C@H](O)CNC(=O)C[C@@H]1C[C@H]1C1CC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 6, 7, 7, 7, 27, 46, 46, 46, 46, 46, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 6, 6, 7, 27, 27, 46, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338450236 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450236 Building ZINC001338450541 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338450541 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/227 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338450541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338450541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338450541 none CN(C[C@@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 4, 6, 6, 6, 11, 20, 20, 25, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 18, 11, 11, 20, 50, 50, 50, 50, 50, 50, 50, 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: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/228 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/228' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338450541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338450541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338450541 none CN(C[C@@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 3, 4, 4, 4, 7, 17, 17, 20, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 12, 7, 7, 17, 50, 50, 50, 50, 50, 50, 50, 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: 166 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338450541 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541 Building ZINC001338450541 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338450541 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 227) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338450541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338450541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338450541 none CN(C[C@@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 4, 6, 6, 6, 11, 20, 20, 25, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 18, 11, 11, 20, 50, 50, 50, 50, 50, 50, 50, 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: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 228) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338450541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338450541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338450541 none CN(C[C@@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 3, 4, 4, 4, 7, 17, 17, 20, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 12, 7, 7, 17, 50, 50, 50, 50, 50, 50, 50, 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: 166 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338450541 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450541 Building ZINC001338450543 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338450543 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/229 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338450543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338450543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338450543 none CN(C[C@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 3, 4, 4, 4, 8, 13, 13, 16, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 12, 8, 8, 13, 50, 50, 50, 50, 50, 50, 50, 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: 159 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/230 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338450543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338450543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338450543 none CN(C[C@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 4, 6, 6, 6, 11, 16, 16, 21, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 18, 11, 11, 16, 50, 50, 50, 50, 50, 50, 50, 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: 181 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338450543 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543 Building ZINC001338450543 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338450543 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 229) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338450543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338450543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338450543 none CN(C[C@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 3, 4, 4, 4, 8, 13, 13, 16, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 12, 8, 8, 13, 50, 50, 50, 50, 50, 50, 50, 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: 159 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 230) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338450543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338450543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338450543 none CN(C[C@H](O)CNC(=O)C1(C)CC(F)(F)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 4, 6, 6, 6, 11, 16, 16, 21, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 18, 11, 11, 16, 50, 50, 50, 50, 50, 50, 50, 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: 181 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338450543 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450543 Building ZINC001338450668 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338450668 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/231 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ns1) `ZINC001338450668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338450668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338450668 none Cc1cc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ns1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 14, 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, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 9, 5, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 31, 27, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 218 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/232 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ns1) `ZINC001338450668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338450668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338450668 none Cc1cc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ns1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 14, 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, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 30, 30, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 227 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338450668 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668 Building ZINC001338450668 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338450668 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 231) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ns1) `ZINC001338450668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338450668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338450668 none Cc1cc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ns1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 14, 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, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 9, 5, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 31, 27, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 218 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 232) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ns1) `ZINC001338450668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338450668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338450668 none Cc1cc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ns1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 14, 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, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 30, 30, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 227 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338450668 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450668 Building ZINC001338450674 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338450674 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/233 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ns1) `ZINC001338450674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338450674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338450674 none Cc1cc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ns1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 14, 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, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 30, 30, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 227 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/234 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ns1) `ZINC001338450674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338450674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338450674 none Cc1cc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ns1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 14, 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, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 9, 5, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 31, 27, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 218 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338450674 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674 Building ZINC001338450674 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338450674 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 233) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ns1) `ZINC001338450674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338450674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338450674 none Cc1cc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ns1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 14, 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, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 30, 30, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 227 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 234) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ns1) `ZINC001338450674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338450674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338450674 none Cc1cc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ns1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 14, 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, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 9, 5, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 31, 27, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 218 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338450674 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338450674 Building ZINC001338451234 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451234 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/235 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccn1C) `ZINC001338451234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338451234 none Cc1c(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccn1C 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 32, 32, 19, 9, 7, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 32, 19, 19, 27, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/236 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ccn1C) `ZINC001338451234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338451234 none Cc1c(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ccn1C 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 24, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 33, 24, 24, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 200 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451234 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234 Building ZINC001338451234 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451234 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 235) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1c(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccn1C) `ZINC001338451234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338451234 none Cc1c(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccn1C 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 32, 32, 19, 9, 7, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 32, 19, 19, 27, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 236) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1c(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ccn1C) `ZINC001338451234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338451234 none Cc1c(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ccn1C 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 24, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 33, 24, 24, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 200 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451234 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451234 Building ZINC001338451235 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451235 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/237 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccn1C) `ZINC001338451235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338451235 none Cc1c(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccn1C 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 24, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 33, 24, 24, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 200 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/238 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ccn1C) `ZINC001338451235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338451235 none Cc1c(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ccn1C 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 20, 9, 7, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 33, 20, 20, 27, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451235 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235 Building ZINC001338451235 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451235 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 237) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1c(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccn1C) `ZINC001338451235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338451235 none Cc1c(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccn1C 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 24, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 33, 24, 24, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 200 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 238) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1c(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ccn1C) `ZINC001338451235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338451235 none Cc1c(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)ccn1C 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 20, 9, 7, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 33, 20, 20, 27, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451235 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451235 Building ZINC001338451306 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451306 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/239 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c(C)c1C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338451306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338451306 none Cc1n[nH]c(C)c1C(=O)NC[C@@H](O)CN(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 39, 39, 39, 20, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 39, 20, 20, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/240 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c(C)c1C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338451306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338451306 none Cc1n[nH]c(C)c1C(=O)NC[C@@H](O)CN(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 9, 6, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 38, 20, 20, 27, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451306 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306 Building ZINC001338451306 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451306 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 239) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1n[nH]c(C)c1C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338451306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338451306 none Cc1n[nH]c(C)c1C(=O)NC[C@@H](O)CN(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 39, 39, 39, 20, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 39, 20, 20, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 240) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1n[nH]c(C)c1C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338451306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338451306 none Cc1n[nH]c(C)c1C(=O)NC[C@@H](O)CN(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 9, 6, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 38, 20, 20, 27, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451306 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451306 Building ZINC001338451307 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451307 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/241 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c(C)c1C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338451307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338451307 none Cc1n[nH]c(C)c1C(=O)NC[C@H](O)CN(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 20, 8, 6, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 20, 20, 24, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/242 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c(C)c1C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338451307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338451307 none Cc1n[nH]c(C)c1C(=O)NC[C@H](O)CN(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 39, 39, 39, 21, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 39, 21, 21, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 208 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451307 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307 Building ZINC001338451307 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451307 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 241) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1n[nH]c(C)c1C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338451307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338451307 none Cc1n[nH]c(C)c1C(=O)NC[C@H](O)CN(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 20, 8, 6, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 20, 20, 24, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 242) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1n[nH]c(C)c1C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338451307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338451307 none Cc1n[nH]c(C)c1C(=O)NC[C@H](O)CN(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 39, 39, 39, 21, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 39, 21, 21, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 208 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451307 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451307 Building ZINC001338451443 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451443 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/243 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338451443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338451443 none Cc1cccnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 45, 45, 25, 6, 5, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 25, 25, 18, 5, 5, 3, 3, 3, 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: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/244 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338451443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338451443 none Cc1cccnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 45, 45, 23, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 23, 23, 30, 7, 7, 3, 3, 3, 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: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451443 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443 Building ZINC001338451443 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451443 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 243) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338451443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338451443 none Cc1cccnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 45, 45, 25, 6, 5, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 25, 25, 18, 5, 5, 3, 3, 3, 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: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 244) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338451443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338451443 none Cc1cccnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 45, 45, 23, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 23, 23, 30, 7, 7, 3, 3, 3, 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: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451443 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451443 Building ZINC001338451442 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451442 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/245 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338451442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338451442 none Cc1cccnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 45, 45, 22, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 22, 22, 30, 7, 7, 3, 3, 3, 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: 208 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/246 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338451442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338451442 none Cc1cccnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 46, 46, 46, 24, 6, 5, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 24, 24, 18, 5, 5, 3, 3, 3, 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: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451442 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442 Building ZINC001338451442 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451442 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 245) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338451442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338451442 none Cc1cccnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 45, 45, 22, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 22, 22, 30, 7, 7, 3, 3, 3, 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: 208 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 246) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338451442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338451442 none Cc1cccnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 46, 46, 46, 24, 6, 5, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 24, 24, 18, 5, 5, 3, 3, 3, 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: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451442 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451442 Building ZINC001338451943 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451943 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/247 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)c1nccs1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338451943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338451943 none CN(C[C@H](O)CNC(=O)c1nccs1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 1, 1, 14, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 7, 12, 12, 12, 28, 42, 42, 42, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 36, 28, 28, 42, 50, 50, 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: 230 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/248 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)c1nccs1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338451943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338451943 none CN(C[C@H](O)CNC(=O)c1nccs1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 1, 1, 14, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 7, 10, 10, 10, 23, 44, 44, 44, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 30, 23, 23, 44, 50, 50, 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: 207 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451943 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943 Building ZINC001338451943 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451943 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 247) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)c1nccs1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338451943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338451943 none CN(C[C@H](O)CNC(=O)c1nccs1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 1, 1, 14, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 7, 12, 12, 12, 28, 42, 42, 42, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 36, 28, 28, 42, 50, 50, 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: 230 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 248) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)c1nccs1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338451943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338451943 none CN(C[C@H](O)CNC(=O)c1nccs1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 1, 1, 14, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 7, 10, 10, 10, 23, 44, 44, 44, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 30, 23, 23, 44, 50, 50, 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: 207 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451943 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451943 Building ZINC001338451945 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451945 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/249 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)c1nccs1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338451945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338451945 none CN(C[C@@H](O)CNC(=O)c1nccs1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 1, 1, 14, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 7, 11, 11, 11, 25, 43, 43, 43, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 33, 25, 25, 43, 50, 50, 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: 221 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/250 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/250' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)c1nccs1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338451945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338451945 none CN(C[C@@H](O)CNC(=O)c1nccs1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 1, 1, 14, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 8, 13, 13, 13, 26, 41, 41, 41, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 39, 26, 26, 41, 50, 50, 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: 226 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451945 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945 Building ZINC001338451945 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338451945 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 249) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)c1nccs1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338451945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338451945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338451945 none CN(C[C@@H](O)CNC(=O)c1nccs1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 1, 1, 14, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 7, 11, 11, 11, 25, 43, 43, 43, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 33, 25, 25, 43, 50, 50, 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: 221 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 250) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)c1nccs1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338451945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338451945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338451945 none CN(C[C@@H](O)CNC(=O)c1nccs1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 1, 1, 14, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 8, 13, 13, 13, 26, 41, 41, 41, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 39, 26, 26, 41, 50, 50, 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: 226 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338451945 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338451945 Building ZINC001338452608 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338452608 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/251 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338452608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338452608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338452608 none CCn1ccc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 33, 32, 32, 32, 23, 15, 10, 15, 15, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 33, 33, 32, 23, 23, 45, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 282 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/252 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/252' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338452608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338452608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338452608 none CCn1ccc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 30, 30, 30, 30, 30, 30, 30, 19, 13, 8, 13, 13, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 30, 30, 30, 19, 19, 39, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 275 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338452608 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608 Building ZINC001338452608 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338452608 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 251) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1ccc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338452608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338452608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338452608 none CCn1ccc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 33, 32, 32, 32, 23, 15, 10, 15, 15, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 33, 33, 32, 23, 23, 45, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 282 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 252) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1ccc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338452608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338452608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338452608 none CCn1ccc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 30, 30, 30, 30, 30, 30, 30, 19, 13, 8, 13, 13, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 30, 30, 30, 19, 19, 39, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 275 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338452608 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452608 Building ZINC001338452610 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338452610 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/253 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338452610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338452610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338452610 none CCn1ccc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 31, 31, 31, 31, 31, 31, 20, 14, 9, 14, 14, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 31, 31, 31, 20, 20, 42, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 278 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/254 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338452610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338452610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338452610 none CCn1ccc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 33, 32, 32, 32, 23, 15, 10, 15, 15, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 33, 33, 32, 23, 23, 45, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 282 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338452610 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610 Building ZINC001338452610 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338452610 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 253) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1ccc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338452610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338452610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338452610 none CCn1ccc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 31, 31, 31, 31, 31, 31, 20, 14, 9, 14, 14, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 31, 31, 31, 20, 20, 42, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 278 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 254) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1ccc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338452610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338452610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338452610 none CCn1ccc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 33, 32, 32, 32, 23, 15, 10, 15, 15, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 33, 33, 32, 23, 23, 45, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 282 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338452610 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338452610 Building ZINC001338453392 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338453392 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/255 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ocnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338453392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338453392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338453392 none CCc1ocnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.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.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, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need 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, 46, 46, 46, 46, 34, 34, 34, 16, 7, 5, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 34, 16, 16, 21, 5, 5, 3, 3, 3, 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: 200 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/256 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ocnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338453392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338453392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338453392 none CCc1ocnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.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.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, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 45, 45, 45, 45, 34, 34, 34, 16, 9, 7, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 34, 16, 16, 27, 7, 7, 3, 3, 3, 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: 201 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338453392 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392 Building ZINC001338453392 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338453392 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 255) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1ocnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338453392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338453392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338453392 none CCc1ocnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.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.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, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need 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, 46, 46, 46, 46, 34, 34, 34, 16, 7, 5, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 34, 16, 16, 21, 5, 5, 3, 3, 3, 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: 200 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 256) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1ocnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338453392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338453392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338453392 none CCc1ocnc1C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.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.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, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 45, 45, 45, 45, 34, 34, 34, 16, 9, 7, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 34, 16, 16, 27, 7, 7, 3, 3, 3, 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: 201 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338453392 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453392 Building ZINC001338453393 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338453393 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/257 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ocnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338453393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338453393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338453393 none CCc1ocnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.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.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, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 45, 45, 45, 45, 34, 34, 34, 16, 9, 7, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 34, 16, 16, 27, 7, 7, 3, 3, 3, 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: 201 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/258 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ocnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338453393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338453393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338453393 none CCc1ocnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.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.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, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need 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, 47, 47, 47, 47, 35, 35, 35, 16, 7, 5, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 47, 35, 16, 16, 21, 5, 5, 3, 3, 3, 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: 198 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338453393 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393 Building ZINC001338453393 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338453393 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 257) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1ocnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338453393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338453393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338453393 none CCc1ocnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.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.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, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 45, 45, 45, 45, 34, 34, 34, 16, 9, 7, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 34, 16, 16, 27, 7, 7, 3, 3, 3, 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: 201 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 258) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1ocnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338453393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338453393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338453393 none CCc1ocnc1C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.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.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, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need 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, 47, 47, 47, 47, 35, 35, 35, 16, 7, 5, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 47, 35, 16, 16, 21, 5, 5, 3, 3, 3, 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: 198 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338453393 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338453393 Building ZINC001338455778 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338455778 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/259 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(C)c1C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338455778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338455778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455778 none Cc1cncc(C)c1C(=O)NC[C@@H](O)CN(C)C(=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.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 12, 7, 12, 12, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 36, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 227 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/260 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/260' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(C)c1C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338455778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338455778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455778 none Cc1cncc(C)c1C(=O)NC[C@@H](O)CN(C)C(=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.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 10, 6, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 30, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 218 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338455778 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778 Building ZINC001338455778 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338455778 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 259) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cncc(C)c1C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338455778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338455778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455778 none Cc1cncc(C)c1C(=O)NC[C@@H](O)CN(C)C(=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.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 12, 7, 12, 12, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 36, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 227 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 260) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cncc(C)c1C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338455778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338455778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455778 none Cc1cncc(C)c1C(=O)NC[C@@H](O)CN(C)C(=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.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 10, 6, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 30, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 218 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338455778 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455778 Building ZINC001338455779 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338455779 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/261 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(C)c1C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338455779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338455779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455779 none Cc1cncc(C)c1C(=O)NC[C@H](O)CN(C)C(=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.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 218 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/262 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(C)c1C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338455779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338455779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455779 none Cc1cncc(C)c1C(=O)NC[C@H](O)CN(C)C(=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.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 12, 7, 12, 12, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 36, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 228 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338455779 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779 Building ZINC001338455779 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338455779 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 261) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cncc(C)c1C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338455779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338455779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455779 none Cc1cncc(C)c1C(=O)NC[C@H](O)CN(C)C(=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.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 218 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 262) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cncc(C)c1C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338455779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338455779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455779 none Cc1cncc(C)c1C(=O)NC[C@H](O)CN(C)C(=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.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 12, 7, 12, 12, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 36, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 228 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338455779 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455779 Building ZINC001338455894 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338455894 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/263 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338455894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338455894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455894 none CN(C[C@@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 5, 5, 5, 9, 15, 15, 15, 39, 41, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 9, 9, 15, 39, 39, 41, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [0, 1, 2, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 214 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/264 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/264' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338455894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338455894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455894 none CN(C[C@@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 5, 5, 5, 7, 14, 14, 14, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 7, 7, 14, 32, 32, 36, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [0, 1, 2, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 201 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338455894 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894 Building ZINC001338455894 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338455894 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 263) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338455894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338455894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455894 none CN(C[C@@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 5, 5, 5, 9, 15, 15, 15, 39, 41, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 9, 9, 15, 39, 39, 41, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [0, 1, 2, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 214 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 264) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338455894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338455894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455894 none CN(C[C@@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 5, 5, 5, 7, 14, 14, 14, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 7, 7, 14, 32, 32, 36, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [0, 1, 2, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 201 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338455894 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455894 Building ZINC001338455895 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338455895 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/265 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338455895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338455895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455895 none CN(C[C@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 5, 5, 5, 7, 14, 14, 14, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 7, 7, 14, 32, 32, 36, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [0, 1, 2, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 201 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/266 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338455895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338455895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455895 none CN(C[C@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 5, 5, 5, 9, 15, 15, 15, 38, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 9, 9, 15, 38, 38, 40, 40, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [0, 1, 2, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338455895 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895 Building ZINC001338455895 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338455895 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 265) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338455895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338455895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455895 none CN(C[C@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 5, 5, 5, 7, 14, 14, 14, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 7, 7, 14, 32, 32, 36, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [0, 1, 2, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 201 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 266) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338455895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338455895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338455895 none CN(C[C@H](O)CNC(=O)CCc1cccnc1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 5, 5, 5, 9, 15, 15, 15, 38, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 9, 9, 15, 38, 38, 40, 40, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [0, 1, 2, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338455895 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338455895 Building ZINC001338457300 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338457300 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/267 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338457300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457300 none CO[C@@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 32, 19, 19, 9, 6, 5, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 32, 32, 32, 19, 9, 9, 18, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/268 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338457300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457300 none CO[C@@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 34, 16, 34, 16, 16, 6, 4, 4, 4, 4, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 35, 35, 35, 16, 6, 6, 12, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338457300 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300 Building ZINC001338457300 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338457300 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 267) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338457300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457300 none CO[C@@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 32, 19, 19, 9, 6, 5, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 32, 32, 32, 19, 9, 9, 18, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 268) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338457300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457300 none CO[C@@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 34, 16, 34, 16, 16, 6, 4, 4, 4, 4, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 35, 35, 35, 16, 6, 6, 12, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338457300 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457300 Building ZINC001338457302 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338457302 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/269 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338457302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457302 none CO[C@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 18, 36, 18, 18, 9, 6, 5, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 36, 36, 36, 18, 9, 9, 18, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/270 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/270' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338457302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457302 none CO[C@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 36, 18, 36, 18, 18, 5, 3, 3, 3, 3, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 37, 37, 37, 18, 5, 5, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338457302 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302 Building ZINC001338457302 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338457302 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 269) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338457302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457302 none CO[C@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 18, 36, 18, 18, 9, 6, 5, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 36, 36, 36, 18, 9, 9, 18, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 270) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338457302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457302 none CO[C@H](C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 36, 18, 36, 18, 18, 5, 3, 3, 3, 3, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 37, 37, 37, 18, 5, 5, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338457302 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457302 Building ZINC001338457304 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338457304 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/271 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338457304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457304 none CO[C@@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 34, 17, 34, 17, 17, 5, 3, 3, 3, 3, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 35, 35, 35, 17, 5, 5, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 190 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/272 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/272' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338457304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457304 none CO[C@@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 37, 18, 18, 9, 6, 5, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 37, 37, 37, 18, 9, 9, 18, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 216 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338457304 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304 Building ZINC001338457304 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338457304 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 271) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338457304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457304 none CO[C@@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 34, 17, 34, 17, 17, 5, 3, 3, 3, 3, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 35, 35, 35, 17, 5, 5, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 190 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 272) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338457304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457304 none CO[C@@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 37, 18, 18, 9, 6, 5, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 37, 37, 37, 18, 9, 9, 18, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 216 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338457304 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457304 Building ZINC001338457306 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338457306 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/273 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338457306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457306 none CO[C@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 34, 16, 34, 16, 16, 6, 4, 4, 4, 4, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 35, 35, 35, 16, 6, 6, 12, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/274 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338457306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457306 none CO[C@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 20, 34, 20, 20, 10, 6, 5, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 34, 34, 34, 20, 10, 10, 18, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 220 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338457306 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306 Building ZINC001338457306 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338457306 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 273) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338457306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457306 none CO[C@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 34, 16, 34, 16, 16, 6, 4, 4, 4, 4, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 35, 35, 35, 16, 6, 6, 12, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 274) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001338457306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338457306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457306 none CO[C@H](C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 20, 34, 20, 20, 10, 6, 5, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 34, 34, 34, 20, 10, 10, 18, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 220 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338457306 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457306 Building ZINC001338457809 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338457809 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/275 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cs1) `ZINC001338457809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338457809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457809 none Cc1nc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cs1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 10, 6, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 30, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 220 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/276 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/276' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cs1) `ZINC001338457809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338457809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457809 none Cc1nc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cs1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 233 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338457809 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809 Building ZINC001338457809 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338457809 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 275) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cs1) `ZINC001338457809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338457809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457809 none Cc1nc(C(=O)NC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cs1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 10, 6, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 30, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 220 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 276) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cs1) `ZINC001338457809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338457809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457809 none Cc1nc(C(=O)NC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cs1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 233 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338457809 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457809 Building ZINC001338457810 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338457810 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/277 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cs1) `ZINC001338457810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338457810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457810 none Cc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cs1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 233 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/278 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cs1) `ZINC001338457810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338457810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457810 none Cc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cs1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 10, 6, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 30, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 220 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338457810 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810 Building ZINC001338457810 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338457810 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 277) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cs1) `ZINC001338457810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338457810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457810 none Cc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cs1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 233 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 278) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cs1) `ZINC001338457810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338457810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338457810 none Cc1nc(C(=O)NC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cs1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 10, 6, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 30, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 220 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338457810 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338457810 Building ZINC001338465260 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338465260 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/279 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)CCO2)cc1Cl) `ZINC001338465260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338465260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001338465260 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)CCO2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 6, 10, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 11, 11, 11, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/280 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)CCO2)cc1Cl) `ZINC001338465260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338465260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001338465260 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)CCO2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 5, 9, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 11, 11, 11, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338465260 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260 Building ZINC001338465260 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338465260 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 279) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)CCO2)cc1Cl) `ZINC001338465260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338465260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001338465260 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)CCO2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 6, 10, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 11, 11, 11, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 280) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)CCO2)cc1Cl) `ZINC001338465260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338465260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001338465260 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)CCO2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 5, 9, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 11, 11, 11, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338465260 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338465260 Building ZINC001338472392 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338472392 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/281 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1) `ZINC001338472392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338472392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338472392 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 10, 7, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 24, 24, 24, 24, 50, 50, 50, 50, 15, 15, 15, 14, 14, 30, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/282 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/282' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1) `ZINC001338472392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338472392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338472392 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 12, 6, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 24, 24, 24, 24, 50, 50, 50, 50, 14, 14, 14, 14, 14, 36, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338472392 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392 Building ZINC001338472392 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338472392 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 281) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1) `ZINC001338472392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338472392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338472392 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 10, 7, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 24, 24, 24, 24, 50, 50, 50, 50, 15, 15, 15, 14, 14, 30, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 282) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1) `ZINC001338472392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338472392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338472392 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 12, 6, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 24, 24, 24, 24, 50, 50, 50, 50, 14, 14, 14, 14, 14, 36, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338472392 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472392 Building ZINC001338472393 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338472393 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/283 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1) `ZINC001338472393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338472393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338472393 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 12, 6, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 24, 24, 24, 24, 50, 50, 50, 50, 14, 14, 14, 14, 14, 36, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/284 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/284' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1) `ZINC001338472393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338472393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338472393 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 10, 7, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 24, 24, 24, 24, 50, 50, 50, 50, 15, 15, 15, 14, 14, 30, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338472393 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393 Building ZINC001338472393 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338472393 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 283) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1) `ZINC001338472393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338472393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338472393 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 12, 6, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 24, 24, 24, 24, 50, 50, 50, 50, 14, 14, 14, 14, 14, 36, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 284) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1) `ZINC001338472393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338472393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338472393 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccoc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 10, 7, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 24, 24, 24, 24, 50, 50, 50, 50, 15, 15, 15, 14, 14, 30, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338472393 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338472393 Building ZINC001338474474 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338474474 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/285 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nccc1C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338474474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338474474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338474474 none CCn1nccc1C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 36, 36, 36, 26, 19, 26, 19, 19, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 36, 36, 19, 19, 19, 19, 19, 36, 7, 7, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/286 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/286' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nccc1C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338474474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338474474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338474474 none CCn1nccc1C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 41, 41, 41, 41, 29, 18, 29, 16, 18, 8, 5, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 41, 18, 18, 18, 16, 16, 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: 227 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338474474 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474 Building ZINC001338474474 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338474474 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 285) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1nccc1C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338474474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338474474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338474474 none CCn1nccc1C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 36, 36, 36, 26, 19, 26, 19, 19, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 36, 36, 19, 19, 19, 19, 19, 36, 7, 7, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 286) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1nccc1C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338474474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338474474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338474474 none CCn1nccc1C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 41, 41, 41, 41, 29, 18, 29, 16, 18, 8, 5, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 41, 18, 18, 18, 16, 16, 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: 227 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338474474 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474474 Building ZINC001338474475 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338474475 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/287 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nccc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338474475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338474475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338474475 none CCn1nccc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 41, 41, 41, 41, 29, 18, 29, 16, 18, 8, 5, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 41, 18, 18, 18, 16, 16, 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: 227 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/288 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/288' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nccc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338474475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338474475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338474475 none CCn1nccc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 36, 36, 36, 27, 20, 27, 20, 20, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 36, 36, 20, 20, 20, 20, 20, 36, 7, 7, 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: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338474475 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475 Building ZINC001338474475 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338474475 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 287) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1nccc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338474475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338474475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338474475 none CCn1nccc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 41, 41, 41, 41, 29, 18, 29, 16, 18, 8, 5, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 41, 18, 18, 18, 16, 16, 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: 227 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 288) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1nccc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338474475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338474475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338474475 none CCn1nccc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 36, 36, 36, 27, 20, 27, 20, 20, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 36, 36, 20, 20, 20, 20, 20, 36, 7, 7, 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: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338474475 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338474475 Building ZINC001338481550 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338481550 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/289 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338481550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338481550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338481550 none Cc1nc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 46, 31, 46, 25, 31, 15, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 31, 31, 31, 25, 25, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 244 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/290 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338481550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338481550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338481550 none Cc1nc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 47, 35, 47, 30, 35, 21, 10, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 35, 35, 35, 30, 30, 66, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338481550 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550 Building ZINC001338481550 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338481550 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 289) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338481550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338481550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338481550 none Cc1nc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 46, 31, 46, 25, 31, 15, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 31, 31, 31, 25, 25, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 244 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 290) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338481550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338481550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338481550 none Cc1nc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 47, 35, 47, 30, 35, 21, 10, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 35, 35, 35, 30, 30, 66, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338481550 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481550 Building ZINC001338481551 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338481551 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/291 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338481551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338481551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338481551 none Cc1nc(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 47, 36, 47, 31, 36, 22, 11, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 36, 36, 36, 31, 31, 69, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/292 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338481551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338481551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338481551 none Cc1nc(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 46, 31, 46, 25, 31, 15, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 31, 31, 31, 25, 25, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 244 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338481551 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551 Building ZINC001338481551 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338481551 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 291) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338481551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338481551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338481551 none Cc1nc(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 47, 36, 47, 31, 36, 22, 11, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 36, 36, 36, 31, 31, 69, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 292) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001338481551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338481551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001338481551 none Cc1nc(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 46, 31, 46, 25, 31, 15, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 31, 31, 31, 25, 25, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 244 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338481551 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338481551 Building ZINC001338499677 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338499677 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/293 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 50, 32, 32, 31, 32, 17, 12, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 31, 31, 57, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 284 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/294 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/294' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 49, 49, 49, 22, 49, 22, 22, 22, 22, 12, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 22, 22, 22, 22, 22, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 244 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/295 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/295' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 50, 34, 34, 34, 34, 23, 12, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 69, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/296 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/296' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 50, 22, 22, 22, 22, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338499677 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 Building ZINC001338499677 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338499677 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 293) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 50, 32, 32, 31, 32, 17, 12, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 31, 31, 57, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 284 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 294) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 49, 49, 49, 22, 49, 22, 22, 22, 22, 12, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 22, 22, 22, 22, 22, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 244 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 295) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 50, 34, 34, 34, 34, 23, 12, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 69, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 296) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 50, 22, 22, 22, 22, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338499677 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 Building ZINC001338499677 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338499677 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 293) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 50, 32, 32, 31, 32, 17, 12, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 31, 31, 57, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 284 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 294) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 49, 49, 49, 22, 49, 22, 22, 22, 22, 12, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 22, 22, 22, 22, 22, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 244 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 295) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 50, 34, 34, 34, 34, 23, 12, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 69, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 296) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 50, 22, 22, 22, 22, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338499677 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 Building ZINC001338499677 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338499677 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 293) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 50, 32, 32, 31, 32, 17, 12, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 31, 31, 57, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 284 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 294) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 49, 49, 49, 22, 49, 22, 22, 22, 22, 12, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 22, 22, 22, 22, 22, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 244 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 295) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 50, 34, 34, 34, 34, 23, 12, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 69, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 296) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499677.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338499677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499677 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 50, 22, 22, 22, 22, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338499677 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499677 Building ZINC001338499679 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338499679 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/297 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 33, 50, 33, 33, 33, 33, 21, 11, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 63, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/298 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/298' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 23, 50, 23, 23, 23, 23, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/299 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/299' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 33, 50, 33, 33, 32, 33, 19, 12, 20, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 32, 32, 60, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 283 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/300 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/300' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 49, 49, 49, 23, 49, 23, 23, 23, 23, 13, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 23, 23, 23, 23, 23, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 244 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338499679 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 Building ZINC001338499679 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338499679 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 297) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 33, 50, 33, 33, 33, 33, 21, 11, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 63, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 298) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 23, 50, 23, 23, 23, 23, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 299) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 33, 50, 33, 33, 32, 33, 19, 12, 20, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 32, 32, 60, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 283 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 300) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 49, 49, 49, 23, 49, 23, 23, 23, 23, 13, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 23, 23, 23, 23, 23, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 244 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338499679 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 Building ZINC001338499679 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338499679 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 297) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 33, 50, 33, 33, 33, 33, 21, 11, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 63, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 298) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 23, 50, 23, 23, 23, 23, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 299) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 33, 50, 33, 33, 32, 33, 19, 12, 20, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 32, 32, 60, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 283 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 300) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 49, 49, 49, 23, 49, 23, 23, 23, 23, 13, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 23, 23, 23, 23, 23, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 244 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338499679 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 Building ZINC001338499679 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338499679 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 297) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 33, 50, 33, 33, 33, 33, 21, 11, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 63, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 298) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 23, 50, 23, 23, 23, 23, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 299) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 33, 50, 33, 33, 32, 33, 19, 12, 20, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 32, 32, 60, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 283 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 300) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001338499679.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338499679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338499679 none CCO[C@H]1C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 49, 49, 49, 23, 49, 23, 23, 23, 23, 13, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 23, 23, 23, 23, 23, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 244 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338499679 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338499679 Building ZINC001338511141 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338511141 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/301 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001338511141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338511141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338511141 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 17, 10, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 32, 32, 46, 46, 46, 46, 47, 50, 50, 50, 25, 25, 25, 17, 17, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 241 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/302 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/302' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001338511141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338511141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338511141 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 19, 14, 7, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 28, 28, 45, 45, 45, 45, 45, 50, 50, 50, 21, 21, 21, 19, 19, 42, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 249 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338511141 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141 Building ZINC001338511141 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338511141 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 301) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001338511141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338511141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338511141 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 17, 10, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 32, 32, 46, 46, 46, 46, 47, 50, 50, 50, 25, 25, 25, 17, 17, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 241 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 302) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001338511141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338511141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338511141 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 19, 14, 7, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 28, 28, 45, 45, 45, 45, 45, 50, 50, 50, 21, 21, 21, 19, 19, 42, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 249 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338511141 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511141 Building ZINC001338511142 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338511142 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/303 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001338511142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338511142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338511142 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 13, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 28, 28, 43, 43, 43, 43, 44, 50, 50, 50, 23, 23, 23, 19, 19, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 253 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/304 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/304' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001338511142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338511142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338511142 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 15, 10, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 42, 42, 42, 42, 45, 50, 50, 50, 20, 20, 20, 15, 15, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 238 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338511142 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142 Building ZINC001338511142 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338511142 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 303) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001338511142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338511142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338511142 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 13, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 28, 28, 43, 43, 43, 43, 44, 50, 50, 50, 23, 23, 23, 19, 19, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 253 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 304) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001338511142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338511142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338511142 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 15, 10, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 42, 42, 42, 42, 45, 50, 50, 50, 20, 20, 20, 15, 15, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 238 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338511142 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338511142 Building ZINC001338525437 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338525437 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/305 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338525437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338525437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338525437 none CCc1cccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 41, 41, 41, 41, 27, 27, 27, 27, 27, 20, 9, 20, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50, 41, 41, 41, 27, 27, 27, 27, 27, 60, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/306 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/306' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338525437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338525437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338525437 none CCc1cccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 39, 39, 39, 39, 39, 26, 26, 26, 26, 26, 16, 11, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 39, 39, 39, 26, 26, 26, 26, 26, 51, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 270 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338525437 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437 Building ZINC001338525437 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338525437 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 305) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1cccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338525437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338525437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338525437 none CCc1cccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 41, 41, 41, 41, 27, 27, 27, 27, 27, 20, 9, 20, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50, 41, 41, 41, 27, 27, 27, 27, 27, 60, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 306) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1cccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338525437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338525437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338525437 none CCc1cccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 39, 39, 39, 39, 39, 26, 26, 26, 26, 26, 16, 11, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 39, 39, 39, 26, 26, 26, 26, 26, 51, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 270 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338525437 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525437 Building ZINC001338525438 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338525438 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/307 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338525438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338525438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338525438 none CCc1cccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7] 1 hydrogens need 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, 40, 40, 29, 29, 29, 29, 29, 17, 10, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 40, 40, 40, 29, 29, 29, 29, 29, 54, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 281 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/308 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/308' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338525438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338525438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338525438 none CCc1cccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 41, 41, 41, 41, 27, 27, 27, 27, 27, 21, 10, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50, 41, 41, 41, 27, 27, 27, 27, 27, 63, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338525438 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438 Building ZINC001338525438 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338525438 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 307) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1cccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338525438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338525438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338525438 none CCc1cccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7] 1 hydrogens need 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, 40, 40, 29, 29, 29, 29, 29, 17, 10, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 40, 40, 40, 29, 29, 29, 29, 29, 54, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 281 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 308) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1cccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338525438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338525438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338525438 none CCc1cccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 41, 41, 41, 41, 27, 27, 27, 27, 27, 21, 10, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50, 41, 41, 41, 27, 27, 27, 27, 27, 63, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338525438 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338525438 Building ZINC001338530254 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338530254 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/309 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001338530254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338530254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001338530254 none CN(C)C1(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 33, 25, 33, 23, 25, 18, 15, 19, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 23, 23, 57, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 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, 51, 52, 53, 54]) total number of confs: 259 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/310 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/310' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001338530254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338530254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001338530254 none CN(C)C1(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 26, 30, 25, 26, 20, 14, 20, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 25, 25, 60, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 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, 51, 52, 53, 54]) total number of confs: 267 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338530254 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254 Building ZINC001338530254 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338530254 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 309) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)C1(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001338530254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338530254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001338530254 none CN(C)C1(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 33, 25, 33, 23, 25, 18, 15, 19, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 23, 23, 57, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 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, 51, 52, 53, 54]) total number of confs: 259 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 310) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)C1(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001338530254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338530254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001338530254 none CN(C)C1(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 26, 30, 25, 26, 20, 14, 20, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 25, 25, 60, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 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, 51, 52, 53, 54]) total number of confs: 267 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338530254 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530254 Building ZINC001338530256 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338530256 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/311 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001338530256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338530256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001338530256 none CN(C)C1(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 26, 31, 24, 26, 19, 13, 19, 19, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 24, 24, 57, 13, 13, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 269 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/312 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/312' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001338530256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338530256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001338530256 none CN(C)C1(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 37, 29, 37, 27, 29, 18, 15, 19, 19, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 27, 27, 57, 15, 15, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 273 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338530256 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256 Building ZINC001338530256 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338530256 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 311) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)C1(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001338530256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338530256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001338530256 none CN(C)C1(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 26, 31, 24, 26, 19, 13, 19, 19, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 24, 24, 57, 13, 13, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 269 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 312) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)C1(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001338530256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338530256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001338530256 none CN(C)C1(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 37, 29, 37, 27, 29, 18, 15, 19, 19, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 27, 27, 57, 15, 15, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 273 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338530256 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530256 Building ZINC001338530646 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338530646 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/313 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@@H](C)C1) `ZINC001338530646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338530646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338530646 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 17, 40, 26, 44, 44, 44, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/314 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/314' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@@H](C)C1) `ZINC001338530646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338530646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338530646 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 18, 41, 28, 45, 45, 45, 45, 45, 45, 45, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338530646 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646 Building ZINC001338530646 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338530646 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 313) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@@H](C)C1) `ZINC001338530646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338530646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338530646 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 17, 40, 26, 44, 44, 44, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 314) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@@H](C)C1) `ZINC001338530646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338530646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338530646 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 18, 41, 28, 45, 45, 45, 45, 45, 45, 45, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338530646 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530646 Building ZINC001338530674 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338530674 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/315 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@H](C)C1) `ZINC001338530674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338530674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338530674 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 17, 40, 27, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/316 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@H](C)C1) `ZINC001338530674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338530674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338530674 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 18, 18, 40, 26, 44, 44, 44, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338530674 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674 Building ZINC001338530674 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338530674 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 315) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@H](C)C1) `ZINC001338530674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338530674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338530674 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 17, 40, 27, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 316) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@H](C)C1) `ZINC001338530674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338530674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001338530674 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 18, 18, 40, 26, 44, 44, 44, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338530674 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338530674 Building ZINC001338548010 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338548010 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/317 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338548010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548010 none C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 26, 29, 20, 26, 19, 20, 15, 7, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 29, 29, 29, 20, 20, 20, 19, 19, 45, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/318 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338548010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548010 none C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 27, 30, 20, 27, 17, 20, 11, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 30, 30, 30, 20, 20, 20, 17, 17, 36, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338548010 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010 Building ZINC001338548010 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338548010 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 317) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338548010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548010 none C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 26, 29, 20, 26, 19, 20, 15, 7, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 29, 29, 29, 20, 20, 20, 19, 19, 45, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 318) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338548010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548010 none C[C@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 27, 30, 20, 27, 17, 20, 11, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 30, 30, 30, 20, 20, 20, 17, 17, 36, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338548010 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548010 Building ZINC001338548013 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338548013 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/319 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338548013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548013 none C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 30, 39, 24, 30, 23, 24, 11, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 39, 39, 39, 24, 24, 24, 23, 23, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/320 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338548013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548013 none C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens 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, 32, 39, 26, 32, 24, 26, 16, 8, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 39, 39, 39, 26, 26, 26, 24, 24, 48, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 247 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338548013 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013 Building ZINC001338548013 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338548013 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 319) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338548013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548013 none C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 30, 39, 24, 30, 23, 24, 11, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 39, 39, 39, 24, 24, 24, 23, 23, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 320) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338548013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548013 none C[C@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens 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, 32, 39, 26, 32, 24, 26, 16, 8, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 39, 39, 39, 26, 26, 26, 24, 24, 48, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 247 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338548013 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548013 Building ZINC001338548016 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338548016 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/321 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338548016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548016 none C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 27, 30, 20, 27, 17, 20, 11, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 30, 30, 30, 20, 20, 20, 17, 17, 36, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/322 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338548016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548016 none C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 26, 30, 20, 26, 19, 20, 15, 7, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 30, 30, 30, 20, 20, 20, 19, 19, 45, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338548016 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016 Building ZINC001338548016 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338548016 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 321) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338548016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548016 none C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 27, 30, 20, 27, 17, 20, 11, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 30, 30, 30, 20, 20, 20, 17, 17, 36, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 322) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338548016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548016 none C[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 26, 30, 20, 26, 19, 20, 15, 7, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 30, 30, 30, 20, 20, 20, 19, 19, 45, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338548016 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548016 Building ZINC001338548019 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338548019 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/323 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338548019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548019 none C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 30, 36, 24, 30, 22, 24, 15, 7, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 36, 36, 36, 24, 24, 24, 22, 22, 45, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/324 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/324' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338548019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548019 none C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 30, 39, 24, 30, 23, 24, 11, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 39, 39, 39, 24, 24, 24, 23, 23, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338548019 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019 Building ZINC001338548019 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338548019 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 323) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338548019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548019 none C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 30, 36, 24, 30, 22, 24, 15, 7, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 36, 36, 36, 24, 24, 24, 22, 22, 45, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 324) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001338548019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338548019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338548019 none C[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 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, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 30, 39, 24, 30, 23, 24, 11, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 39, 39, 39, 24, 24, 24, 23, 23, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338548019 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338548019 Building ZINC001338549131 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338549131 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/325 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1) `ZINC001338549131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338549131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338549131 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 12, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 48, 48, 49, 50, 50, 49, 49, 31, 31, 31, 19, 19, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 49, 49] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 245 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/326 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1) `ZINC001338549131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338549131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338549131 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 19, 19, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 238 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338549131 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131 Building ZINC001338549131 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338549131 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 325) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1) `ZINC001338549131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338549131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338549131 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 12, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 48, 48, 49, 50, 50, 49, 49, 31, 31, 31, 19, 19, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 49, 49] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 245 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 326) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1) `ZINC001338549131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338549131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338549131 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 19, 19, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 238 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338549131 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549131 Building ZINC001338549132 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338549132 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/327 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1) `ZINC001338549132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338549132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338549132 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 24, 18, 10, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 49, 49, 49, 50, 50, 49, 49, 34, 34, 34, 24, 24, 54, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 49, 49] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 266 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/328 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/328' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1) `ZINC001338549132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338549132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338549132 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 11, 6, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 45, 45, 46, 50, 50, 46, 46, 28, 28, 28, 20, 20, 36, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 46, 46, 46, 46] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 255 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338549132 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132 Building ZINC001338549132 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338549132 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 327) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1) `ZINC001338549132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338549132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338549132 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 24, 18, 10, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 49, 49, 49, 50, 50, 49, 49, 34, 34, 34, 24, 24, 54, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 49, 49] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 266 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 328) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1) `ZINC001338549132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338549132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338549132 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(CCF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 11, 6, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 45, 45, 46, 50, 50, 46, 46, 28, 28, 28, 20, 20, 36, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 46, 46, 46, 46] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 255 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338549132 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338549132 Building ZINC001338551959 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338551959 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/329 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1) `ZINC001338551959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338551959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338551959 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 20, 13, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 42, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 20, 20, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 222 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/330 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1) `ZINC001338551959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338551959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338551959 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 19, 13, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 42, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 19, 19, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338551959 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959 Building ZINC001338551959 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338551959 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 329) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1) `ZINC001338551959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338551959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338551959 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 20, 13, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 42, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 20, 20, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 222 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 330) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1) `ZINC001338551959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338551959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338551959 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 19, 13, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 42, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 19, 19, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338551959 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551959 Building ZINC001338551964 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338551964 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/331 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1) `ZINC001338551964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338551964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338551964 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 19, 7, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 46, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 23, 23, 57, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 254 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/332 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1) `ZINC001338551964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338551964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338551964 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 22, 13, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 41, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 22, 22, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 224 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338551964 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964 Building ZINC001338551964 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338551964 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 331) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1) `ZINC001338551964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338551964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338551964 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 19, 7, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 46, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 23, 23, 57, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 254 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 332) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1) `ZINC001338551964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338551964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338551964 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(C)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 22, 13, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 41, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 22, 22, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 224 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338551964 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338551964 Building ZINC001338580527 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338580527 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/333 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338580527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338580527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338580527 none CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 26, 34, 24, 26, 18, 9, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 24, 24, 54, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/334 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338580527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338580527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338580527 none CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in 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, 47, 50, 17, 32, 14, 17, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 14, 14, 24, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338580527 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527 Building ZINC001338580527 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338580527 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 333) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338580527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338580527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338580527 none CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 26, 34, 24, 26, 18, 9, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 24, 24, 54, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 334) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338580527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338580527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338580527 none CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in 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, 47, 50, 17, 32, 14, 17, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 14, 14, 24, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338580527 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580527 Building ZINC001338580528 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338580528 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/335 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338580528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338580528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338580528 none CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 20, 33, 14, 20, 8, 5, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 14, 14, 27, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/336 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/336' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338580528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338580528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338580528 none CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 23, 32, 22, 23, 15, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 22, 22, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338580528 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528 Building ZINC001338580528 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338580528 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 335) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338580528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338580528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338580528 none CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 20, 33, 14, 20, 8, 5, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 14, 14, 27, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 336) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338580528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338580528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338580528 none CC[C@@H]1OCC[C@H]1C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 23, 32, 22, 23, 15, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 22, 22, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338580528 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338580528 Building ZINC001338586201 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338586201 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/337 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001338586201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338586201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338586201 none COc1ccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 38, 35, 38, 33, 35, 22, 8, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 35, 33, 33, 69, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 270 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/338 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/338' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001338586201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338586201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338586201 none COc1ccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 40, 42, 36, 40, 22, 13, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 40, 36, 36, 72, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 278 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338586201 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201 Building ZINC001338586201 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338586201 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 337) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1ccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001338586201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338586201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338586201 none COc1ccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 38, 35, 38, 33, 35, 22, 8, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 35, 33, 33, 69, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 270 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 338) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1ccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001338586201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338586201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338586201 none COc1ccc(C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 40, 42, 36, 40, 22, 13, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 40, 36, 36, 72, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 278 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338586201 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586201 Building ZINC001338586202 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338586202 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/339 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001338586202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338586202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338586202 none COc1ccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 40, 42, 36, 40, 22, 13, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 40, 36, 36, 72, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 278 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/340 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001338586202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338586202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338586202 none COc1ccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 37, 35, 37, 33, 35, 25, 11, 26, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 35, 33, 33, 78, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 271 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338586202 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202 Building ZINC001338586202 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338586202 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 339) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1ccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001338586202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338586202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338586202 none COc1ccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 42, 40, 42, 36, 40, 22, 13, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 40, 36, 36, 72, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 278 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 340) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1ccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001338586202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338586202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338586202 none COc1ccc(C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 37, 35, 37, 33, 35, 25, 11, 26, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 35, 33, 33, 78, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 271 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338586202 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338586202 Building ZINC001338599458 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338599458 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/341 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccoc1CC(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338599458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338599458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599458 none Cc1ccoc1CC(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 39, 24, 19, 24, 18, 19, 14, 9, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 39, 39, 19, 19, 19, 18, 18, 42, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/342 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccoc1CC(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338599458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338599458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599458 none Cc1ccoc1CC(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 35, 19, 14, 19, 11, 14, 7, 4, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 11, 11, 21, 4, 4, 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: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338599458 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458 Building ZINC001338599458 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338599458 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 341) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccoc1CC(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338599458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338599458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599458 none Cc1ccoc1CC(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 39, 24, 19, 24, 18, 19, 14, 9, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 39, 39, 19, 19, 19, 18, 18, 42, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 342) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccoc1CC(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338599458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338599458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599458 none Cc1ccoc1CC(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 35, 19, 14, 19, 11, 14, 7, 4, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 11, 11, 21, 4, 4, 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: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338599458 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599458 Building ZINC001338599459 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338599459 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/343 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccoc1CC(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338599459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338599459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599459 none Cc1ccoc1CC(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 35, 19, 14, 19, 11, 14, 7, 4, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 11, 11, 21, 4, 4, 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: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/344 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccoc1CC(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338599459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338599459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599459 none Cc1ccoc1CC(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 39, 24, 19, 24, 18, 19, 14, 9, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 39, 39, 19, 19, 19, 18, 18, 42, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338599459 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459 Building ZINC001338599459 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338599459 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 343) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccoc1CC(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338599459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338599459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599459 none Cc1ccoc1CC(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 35, 19, 14, 19, 11, 14, 7, 4, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 35, 35, 14, 14, 14, 11, 11, 21, 4, 4, 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: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 344) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccoc1CC(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338599459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338599459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599459 none Cc1ccoc1CC(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 39, 24, 19, 24, 18, 19, 14, 9, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 39, 39, 19, 19, 19, 18, 18, 42, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338599459 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599459 Building ZINC001338599500 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338599500 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/345 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncoc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338599500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338599500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599500 none CCc1ncoc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 48, 48, 48, 48, 25, 15, 25, 14, 15, 7, 5, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 48, 15, 15, 15, 14, 14, 21, 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: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/346 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/346' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncoc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338599500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338599500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599500 none CCc1ncoc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 48, 48, 48, 48, 27, 22, 27, 22, 22, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 48, 22, 22, 22, 22, 22, 36, 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: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338599500 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500 Building ZINC001338599500 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338599500 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 345) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1ncoc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338599500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338599500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599500 none CCc1ncoc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 48, 48, 48, 48, 25, 15, 25, 14, 15, 7, 5, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 48, 15, 15, 15, 14, 14, 21, 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: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 346) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1ncoc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338599500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338599500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599500 none CCc1ncoc1C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 48, 48, 48, 48, 27, 22, 27, 22, 22, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 48, 22, 22, 22, 22, 22, 36, 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: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338599500 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599500 Building ZINC001338599501 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338599501 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/347 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncoc1C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338599501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338599501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599501 none CCc1ncoc1C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 48, 48, 48, 48, 26, 21, 26, 21, 21, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 48, 21, 21, 21, 21, 21, 36, 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/348 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/348' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncoc1C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338599501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338599501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599501 none CCc1ncoc1C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need 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, 49, 49, 49, 49, 25, 16, 25, 15, 16, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 16, 16, 16, 15, 15, 24, 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: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338599501 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501 Building ZINC001338599501 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338599501 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 347) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1ncoc1C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338599501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338599501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599501 none CCc1ncoc1C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 48, 48, 48, 48, 26, 21, 26, 21, 21, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 48, 21, 21, 21, 21, 21, 36, 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 348) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1ncoc1C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338599501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338599501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338599501 none CCc1ncoc1C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need 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, 49, 49, 49, 49, 25, 16, 25, 15, 16, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 16, 16, 16, 15, 15, 24, 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: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338599501 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338599501 Building ZINC001338629331 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338629331 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/349 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)on1) `ZINC001338629331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338629331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338629331 none Cc1cc(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 50, 30, 48, 16, 9, 16, 16, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 48, 48, 48, 30, 30, 48, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 255 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/350 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)on1) `ZINC001338629331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338629331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338629331 none Cc1cc(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 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, 45, 49, 34, 45, 14, 7, 14, 14, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 45, 34, 34, 42, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 255 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338629331 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331 Building ZINC001338629331 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338629331 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 349) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cc(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)on1) `ZINC001338629331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338629331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338629331 none Cc1cc(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 50, 30, 48, 16, 9, 16, 16, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 48, 48, 48, 30, 30, 48, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 255 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 350) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cc(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)on1) `ZINC001338629331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338629331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338629331 none Cc1cc(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 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, 45, 49, 34, 45, 14, 7, 14, 14, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 45, 34, 34, 42, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 255 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338629331 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629331 Building ZINC001338629334 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338629334 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/351 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)on1) `ZINC001338629334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338629334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338629334 none Cc1cc(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 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, 45, 49, 34, 45, 15, 8, 15, 15, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 45, 34, 34, 45, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 261 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/352 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)on1) `ZINC001338629334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338629334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338629334 none Cc1cc(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 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, 46, 49, 29, 46, 16, 9, 16, 16, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 46, 29, 29, 48, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 253 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338629334 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334 Building ZINC001338629334 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338629334 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 351) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cc(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)on1) `ZINC001338629334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338629334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338629334 none Cc1cc(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 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, 45, 49, 34, 45, 15, 8, 15, 15, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 45, 34, 34, 45, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 261 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 352) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cc(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)on1) `ZINC001338629334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338629334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001338629334 none Cc1cc(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 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, 46, 49, 29, 46, 16, 9, 16, 16, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 46, 29, 29, 48, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 253 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338629334 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338629334 Building ZINC001338631362 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338631362 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/353 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1) `ZINC001338631362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338631362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338631362 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 12, 6, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 40, 40, 50, 50, 50, 50, 19, 19, 19, 12, 12, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 44]) total number of confs: 184 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/354 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/354' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1) `ZINC001338631362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338631362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338631362 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 11, 8, 4, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 43, 43, 50, 50, 50, 50, 18, 18, 18, 11, 11, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 44]) total number of confs: 186 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338631362 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362 Building ZINC001338631362 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338631362 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 353) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1) `ZINC001338631362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338631362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338631362 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 12, 6, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 40, 40, 50, 50, 50, 50, 19, 19, 19, 12, 12, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 44]) total number of confs: 184 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 354) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1) `ZINC001338631362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338631362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338631362 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 11, 8, 4, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 43, 43, 50, 50, 50, 50, 18, 18, 18, 11, 11, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 44]) total number of confs: 186 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338631362 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631362 Building ZINC001338631363 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338631363 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/355 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1) `ZINC001338631363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338631363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338631363 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 10, 8, 4, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 43, 43, 50, 50, 50, 50, 17, 17, 17, 10, 10, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 44]) total number of confs: 182 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/356 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/356' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1) `ZINC001338631363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338631363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338631363 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 6, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 40, 40, 50, 50, 50, 50, 19, 19, 19, 9, 9, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 44]) total number of confs: 179 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338631363 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363 Building ZINC001338631363 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338631363 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 355) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1) `ZINC001338631363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338631363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338631363 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 10, 8, 4, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 43, 43, 50, 50, 50, 50, 17, 17, 17, 10, 10, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 44]) total number of confs: 182 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 356) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1) `ZINC001338631363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338631363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001338631363 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnsn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 6, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 40, 40, 50, 50, 50, 50, 19, 19, 19, 9, 9, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 150 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 44]) total number of confs: 179 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338631363 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338631363 Building ZINC001338644049 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338644049 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/357 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c[nH]c(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338644049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338644049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338644049 none Cc1c[nH]c(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 37, 46, 15, 7, 15, 15, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 46, 46, 37, 37, 45, 7, 7, 3, 3, 3, 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: 254 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/358 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/358' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c[nH]c(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338644049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338644049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338644049 none Cc1c[nH]c(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 29, 46, 13, 7, 13, 13, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 46, 46, 29, 29, 39, 7, 7, 3, 3, 3, 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: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338644049 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049 Building ZINC001338644049 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338644049 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 357) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1c[nH]c(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338644049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338644049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338644049 none Cc1c[nH]c(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 37, 46, 15, 7, 15, 15, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 46, 46, 37, 37, 45, 7, 7, 3, 3, 3, 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: 254 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 358) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1c[nH]c(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338644049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338644049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338644049 none Cc1c[nH]c(C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 29, 46, 13, 7, 13, 13, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 46, 46, 29, 29, 39, 7, 7, 3, 3, 3, 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: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338644049 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644049 Building ZINC001338644050 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338644050 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/359 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c[nH]c(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338644050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338644050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338644050 none Cc1c[nH]c(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 29, 46, 14, 8, 14, 14, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 46, 46, 29, 29, 42, 8, 8, 3, 3, 3, 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: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/360 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/360' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c[nH]c(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338644050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338644050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338644050 none Cc1c[nH]c(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 37, 46, 14, 6, 14, 14, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 46, 46, 37, 37, 42, 6, 6, 3, 3, 3, 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: 251 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338644050 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050 Building ZINC001338644050 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338644050 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 359) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1c[nH]c(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338644050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338644050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338644050 none Cc1c[nH]c(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 29, 46, 14, 8, 14, 14, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 46, 46, 29, 29, 42, 8, 8, 3, 3, 3, 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: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 360) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1c[nH]c(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001338644050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338644050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338644050 none Cc1c[nH]c(C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 46, 50, 37, 46, 14, 6, 14, 14, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 46, 46, 37, 37, 42, 6, 6, 3, 3, 3, 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: 251 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338644050 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644050 Building ZINC001338644645 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338644645 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/361 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1) `ZINC001338644645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338644645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001338644645 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 15, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 23, 24, 24, 39, 50, 50, 50, 50, 23, 23, 23, 15, 15, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 228 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/362 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/362' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1) `ZINC001338644645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338644645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001338644645 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 12, 9, 7, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 39, 50, 50, 50, 50, 20, 20, 20, 12, 12, 27, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338644645 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645 Building ZINC001338644645 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338644645 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 361) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1) `ZINC001338644645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338644645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001338644645 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 15, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 23, 24, 24, 39, 50, 50, 50, 50, 23, 23, 23, 15, 15, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 228 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 362) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1) `ZINC001338644645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338644645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001338644645 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 12, 9, 7, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 39, 50, 50, 50, 50, 20, 20, 20, 12, 12, 27, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338644645 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644645 Building ZINC001338644646 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338644646 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/363 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1) `ZINC001338644646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338644646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001338644646 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 12, 9, 7, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 39, 50, 50, 50, 50, 20, 20, 20, 12, 12, 27, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/364 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/364' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1) `ZINC001338644646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338644646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001338644646 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 16, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 24, 25, 25, 41, 50, 50, 50, 50, 24, 24, 24, 16, 16, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 233 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338644646 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646 Building ZINC001338644646 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338644646 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 363) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1) `ZINC001338644646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338644646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001338644646 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 12, 9, 7, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 39, 50, 50, 50, 50, 20, 20, 20, 12, 12, 27, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 364) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1) `ZINC001338644646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338644646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001338644646 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 16, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 24, 25, 25, 41, 50, 50, 50, 50, 24, 24, 24, 16, 16, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 233 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338644646 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338644646 Building ZINC001338649795 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338649795 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/365 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]cc1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338649795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338649795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338649795 none Cc1n[nH]cc1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 32, 38, 20, 32, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 32, 32, 32, 20, 20, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 215 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/366 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/366' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]cc1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338649795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338649795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338649795 none Cc1n[nH]cc1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 34, 36, 23, 34, 11, 6, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 34, 34, 34, 23, 23, 33, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 213 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338649795 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795 Building ZINC001338649795 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338649795 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 365) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1n[nH]cc1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338649795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338649795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338649795 none Cc1n[nH]cc1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 32, 38, 20, 32, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 32, 32, 32, 20, 20, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 215 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 366) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1n[nH]cc1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338649795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338649795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338649795 none Cc1n[nH]cc1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 34, 36, 23, 34, 11, 6, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 34, 34, 34, 23, 23, 33, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 213 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338649795 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649795 Building ZINC001338649796 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338649796 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/367 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]cc1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338649796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338649796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338649796 none Cc1n[nH]cc1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 37, 35, 37, 23, 35, 11, 6, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 35, 35, 35, 23, 23, 33, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 213 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/368 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/368' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]cc1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338649796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338649796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338649796 none Cc1n[nH]cc1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 32, 38, 20, 32, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 32, 32, 32, 20, 20, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 215 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338649796 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796 Building ZINC001338649796 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338649796 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 367) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1n[nH]cc1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338649796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338649796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338649796 none Cc1n[nH]cc1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 37, 35, 37, 23, 35, 11, 6, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 35, 35, 35, 23, 23, 33, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 213 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 368) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1n[nH]cc1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338649796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338649796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001338649796 none Cc1n[nH]cc1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 32, 38, 20, 32, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 32, 32, 32, 20, 20, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 215 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338649796 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338649796 Building ZINC001338715498 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338715498 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/369 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)c1nnn(C)n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338715498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338715498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338715498 none CC(C)N(CCN(C)C(=O)c1nnn(C)n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 1, 8, 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, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 11, 11, 28, 28, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 11, 11, 11, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 118 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/370 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/370' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)c1nnn(C)n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338715498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338715498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338715498 none CC(C)N(CCN(C)C(=O)c1nnn(C)n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 1, 8, 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, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 12, 12, 28, 28, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 12, 12, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 120 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338715498 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498 Building ZINC001338715498 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338715498 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 369) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)N(CCN(C)C(=O)c1nnn(C)n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338715498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338715498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338715498 none CC(C)N(CCN(C)C(=O)c1nnn(C)n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 1, 8, 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, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 11, 11, 28, 28, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 11, 11, 11, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 118 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 370) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)N(CCN(C)C(=O)c1nnn(C)n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338715498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338715498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338715498 none CC(C)N(CCN(C)C(=O)c1nnn(C)n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 1, 8, 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, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 12, 12, 28, 28, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 12, 12, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 120 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338715498 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715498 Building ZINC001338715518 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338715518 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/371 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338715518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338715518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338715518 none CC(C)N(CCN(C)C(=O)[C@@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 16, 16, 37, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 16, 16, 16, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/372 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/372' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338715518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338715518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338715518 none CC(C)N(CCN(C)C(=O)[C@@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 17, 17, 38, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 17, 17, 17, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338715518 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518 Building ZINC001338715518 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338715518 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 371) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)N(CCN(C)C(=O)[C@@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338715518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338715518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338715518 none CC(C)N(CCN(C)C(=O)[C@@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 16, 16, 37, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 16, 16, 16, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 372) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)N(CCN(C)C(=O)[C@@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338715518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338715518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338715518 none CC(C)N(CCN(C)C(=O)[C@@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 17, 17, 38, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 17, 17, 17, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338715518 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715518 Building ZINC001338715519 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338715519 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/373 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338715519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338715519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338715519 none CC(C)N(CCN(C)C(=O)[C@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 17, 17, 38, 41, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 17, 17, 17, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 152 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/374 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338715519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338715519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338715519 none CC(C)N(CCN(C)C(=O)[C@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 16, 16, 36, 38, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 16, 16, 16, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 156 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338715519 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519 Building ZINC001338715519 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338715519 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 373) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338715519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338715519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338715519 none CC(C)N(CCN(C)C(=O)[C@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 17, 17, 38, 41, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 17, 17, 17, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 152 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 374) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338715519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338715519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338715519 none CC(C)N(CCN(C)C(=O)[C@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 16, 16, 36, 38, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 16, 16, 16, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 156 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338715519 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338715519 Building ZINC001338790096 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338790096 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/375 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1cncn1) `ZINC001338790096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338790096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338790096 none CC(C)N(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 24, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 19, 22, 22, 38, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/376 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1cncn1) `ZINC001338790096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338790096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338790096 none CC(C)N(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 24, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 19, 22, 22, 38, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338790096 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096 Building ZINC001338790096 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338790096 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 375) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1cncn1) `ZINC001338790096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338790096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338790096 none CC(C)N(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 24, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 19, 22, 22, 38, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 376) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/376: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1cncn1) `ZINC001338790096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338790096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338790096 none CC(C)N(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 24, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 19, 22, 22, 38, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338790096 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338790096 Building ZINC001338841423 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338841423 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/377 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1) `ZINC001338841423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338841423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338841423 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 33, 22, 33, 16, 22, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 20, 27, 27, 27, 27, 27, 27, 33, 33, 33, 16, 16, 3, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/378 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/378' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1) `ZINC001338841423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338841423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338841423 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 21, 31, 15, 21, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 20, 26, 26, 26, 26, 26, 26, 31, 31, 31, 15, 15, 3, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338841423 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423 Building ZINC001338841423 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338841423 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 377) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1) `ZINC001338841423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338841423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338841423 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 33, 22, 33, 16, 22, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 20, 27, 27, 27, 27, 27, 27, 33, 33, 33, 16, 16, 3, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 378) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1) `ZINC001338841423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338841423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338841423 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 21, 31, 15, 21, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 20, 26, 26, 26, 26, 26, 26, 31, 31, 31, 15, 15, 3, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338841423 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841423 Building ZINC001338841424 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338841424 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/379 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1) `ZINC001338841424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338841424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338841424 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 22, 32, 16, 22, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 21, 26, 26, 26, 26, 26, 26, 32, 32, 32, 16, 16, 3, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/380 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1) `ZINC001338841424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338841424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338841424 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 33, 22, 33, 16, 22, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 20, 27, 27, 27, 27, 27, 27, 33, 33, 33, 16, 16, 3, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338841424 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424 Building ZINC001338841424 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338841424 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 379) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1) `ZINC001338841424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338841424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338841424 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 22, 32, 16, 22, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 21, 26, 26, 26, 26, 26, 26, 32, 32, 32, 16, 16, 3, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 380) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1) `ZINC001338841424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338841424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001338841424 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 33, 22, 33, 16, 22, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 20, 27, 27, 27, 27, 27, 27, 33, 33, 33, 16, 16, 3, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338841424 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338841424 Building ZINC001338844015 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338844015 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/381 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C) `ZINC001338844015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338844015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338844015 none Cn1nncc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 37, 37, 15, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 37, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/382 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/382' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C) `ZINC001338844015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338844015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338844015 none Cn1nncc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 36, 17, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 11, 11, 11, 50, 50, 50, 50, 36, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 46, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338844015 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015 Building ZINC001338844015 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338844015 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 381) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nncc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C) `ZINC001338844015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338844015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338844015 none Cn1nncc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 37, 37, 15, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 37, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 382) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nncc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C) `ZINC001338844015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338844015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338844015 none Cn1nncc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 36, 17, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 11, 11, 11, 50, 50, 50, 50, 36, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 46, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338844015 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844015 Building ZINC001338844020 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338844020 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/383 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C) `ZINC001338844020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338844020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338844020 none Cn1nncc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 36, 16, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 50, 50, 50, 50, 36, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/384 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/384' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C) `ZINC001338844020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338844020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338844020 none Cn1nncc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 37, 37, 15, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 50, 50, 50, 50, 37, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338844020 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020 Building ZINC001338844020 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338844020 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 383) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nncc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C) `ZINC001338844020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338844020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338844020 none Cn1nncc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 36, 16, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 50, 50, 50, 50, 36, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 384) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nncc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C) `ZINC001338844020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338844020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001338844020 none Cn1nncc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 37, 37, 15, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 50, 50, 50, 50, 37, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338844020 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844020 Building ZINC001338844699 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338844699 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/385 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](CNC(=O)Cn1nccn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338844699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338844699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338844699 none CC(C)(C)[C@@H](CNC(=O)Cn1nccn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 8, 21, 21, 21, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 21, 50, 50, 50, 50, 2, 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: 213 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/386 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/386' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](CNC(=O)Cn1nccn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338844699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338844699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338844699 none CC(C)(C)[C@@H](CNC(=O)Cn1nccn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 10, 24, 24, 24, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 24, 50, 50, 50, 50, 2, 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: 197 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338844699 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699 Building ZINC001338844699 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338844699 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 385) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](CNC(=O)Cn1nccn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338844699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338844699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338844699 none CC(C)(C)[C@@H](CNC(=O)Cn1nccn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 8, 21, 21, 21, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 21, 50, 50, 50, 50, 2, 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: 213 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 386) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](CNC(=O)Cn1nccn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338844699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338844699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338844699 none CC(C)(C)[C@@H](CNC(=O)Cn1nccn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 10, 24, 24, 24, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 24, 50, 50, 50, 50, 2, 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: 197 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338844699 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844699 Building ZINC001338844700 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338844700 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/387 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](CNC(=O)Cn1nccn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338844700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338844700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338844700 none CC(C)(C)[C@H](CNC(=O)Cn1nccn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 10, 24, 24, 24, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 24, 50, 50, 50, 50, 2, 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: 197 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/388 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](CNC(=O)Cn1nccn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338844700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338844700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338844700 none CC(C)(C)[C@H](CNC(=O)Cn1nccn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 8, 22, 22, 22, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 22, 50, 50, 50, 50, 2, 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: 212 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338844700 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700 Building ZINC001338844700 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338844700 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 387) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](CNC(=O)Cn1nccn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338844700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338844700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338844700 none CC(C)(C)[C@H](CNC(=O)Cn1nccn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 10, 24, 24, 24, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 24, 50, 50, 50, 50, 2, 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: 197 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 388) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](CNC(=O)Cn1nccn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338844700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338844700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338844700 none CC(C)(C)[C@H](CNC(=O)Cn1nccn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 8, 22, 22, 22, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 22, 50, 50, 50, 50, 2, 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: 212 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338844700 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338844700 Building ZINC001338859246 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338859246 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/389 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1) `ZINC001338859246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338859246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338859246 none Cn1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 34, 14, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 39, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/390 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1) `ZINC001338859246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338859246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338859246 none Cn1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 38, 38, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 32, 32, 32, 50, 50, 50, 50, 50, 50, 38, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 200 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338859246 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246 Building ZINC001338859246 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338859246 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 389) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1) `ZINC001338859246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338859246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338859246 none Cn1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 34, 14, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 39, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 390) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1) `ZINC001338859246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338859246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338859246 none Cn1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 38, 38, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 32, 32, 32, 50, 50, 50, 50, 50, 50, 38, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 200 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338859246 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859246 Building ZINC001338859247 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338859247 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/391 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1) `ZINC001338859247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338859247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338859247 none Cn1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 40, 40, 32, 14, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 33, 33, 33, 50, 50, 50, 50, 50, 50, 40, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 192 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/392 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/392' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1) `ZINC001338859247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338859247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338859247 none Cn1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 39, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338859247 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247 Building ZINC001338859247 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338859247 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 391) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1) `ZINC001338859247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338859247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338859247 none Cn1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 40, 40, 32, 14, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 33, 33, 33, 50, 50, 50, 50, 50, 50, 40, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 192 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 392) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1) `ZINC001338859247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338859247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001338859247 none Cn1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 39, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338859247 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338859247 Building ZINC001338951436 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338951436 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/393 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)c1cnccn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338951436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338951436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338951436 none COCCN(CCNC(=O)c1cnccn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 10, 3, 10, 18, 21, 37, 37, 37, 39, 39, 39, 39, 39, 1, 3, 1, 1, 1, 1, 1, 1, 24, 24, 24, 16, 16, 11, 11, 18, 18, 21, 21, 37, 39, 39, 39, 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: 182 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/394 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/394' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)c1cnccn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338951436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338951436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338951436 none COCCN(CCNC(=O)c1cnccn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 11, 10, 3, 10, 19, 22, 38, 38, 38, 40, 40, 40, 40, 40, 1, 3, 1, 1, 1, 1, 1, 1, 23, 23, 23, 15, 15, 11, 11, 19, 19, 22, 22, 38, 40, 40, 40, 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: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338951436 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436 Building ZINC001338951436 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338951436 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 393) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)c1cnccn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338951436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338951436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338951436 none COCCN(CCNC(=O)c1cnccn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 10, 3, 10, 18, 21, 37, 37, 37, 39, 39, 39, 39, 39, 1, 3, 1, 1, 1, 1, 1, 1, 24, 24, 24, 16, 16, 11, 11, 18, 18, 21, 21, 37, 39, 39, 39, 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: 182 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 394) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)c1cnccn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338951436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338951436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338951436 none COCCN(CCNC(=O)c1cnccn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 11, 10, 3, 10, 19, 22, 38, 38, 38, 40, 40, 40, 40, 40, 1, 3, 1, 1, 1, 1, 1, 1, 23, 23, 23, 15, 15, 11, 11, 19, 19, 22, 22, 38, 40, 40, 40, 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: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338951436 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338951436 Building ZINC001338964877 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338964877 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/395 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccncc1) `ZINC001338964877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338964877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001338964877 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 40, 26, 19, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 27, 27, 29, 29, 28, 29, 29, 45, 45, 45, 40, 40, 26, 26, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/396 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccncc1) `ZINC001338964877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338964877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001338964877 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 41, 27, 20, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 29, 29, 28, 29, 29, 45, 45, 45, 41, 41, 27, 27, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338964877 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877 Building ZINC001338964877 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338964877 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 395) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccncc1) `ZINC001338964877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338964877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001338964877 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 40, 26, 19, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 27, 27, 29, 29, 28, 29, 29, 45, 45, 45, 40, 40, 26, 26, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 396) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccncc1) `ZINC001338964877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338964877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001338964877 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 41, 27, 20, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 29, 29, 28, 29, 29, 45, 45, 45, 41, 41, 27, 27, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338964877 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964877 Building ZINC001338964879 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338964879 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/397 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC1(O)CCC1) `ZINC001338964879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338964879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338964879 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 26, 17, 14, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 15, 15, 31, 31, 31, 31, 31, 36, 36, 36, 27, 27, 18, 18, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 93, 31, 31, 31, 31, 31, 31] 150 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 311 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/398 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/398' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC1(O)CCC1) `ZINC001338964879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338964879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338964879 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 26, 18, 15, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 16, 16, 33, 33, 33, 33, 33, 36, 36, 36, 27, 27, 19, 19, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 99, 33, 33, 33, 33, 33, 33] 150 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 315 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338964879 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879 Building ZINC001338964879 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338964879 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 397) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC1(O)CCC1) `ZINC001338964879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338964879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338964879 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 26, 17, 14, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 15, 15, 31, 31, 31, 31, 31, 36, 36, 36, 27, 27, 18, 18, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 93, 31, 31, 31, 31, 31, 31] 150 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 311 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 398) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC1(O)CCC1) `ZINC001338964879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338964879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338964879 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 26, 18, 15, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 16, 16, 33, 33, 33, 33, 33, 36, 36, 36, 27, 27, 19, 19, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 99, 33, 33, 33, 33, 33, 33] 150 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 315 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338964879 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338964879 Building ZINC001338965195 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338965195 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/399 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)c1cccn1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338965195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338965195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338965195 none COCCN(CCNC(=O)c1cccn1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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: [27, 17, 12, 9, 2, 9, 14, 20, 32, 32, 32, 43, 43, 43, 43, 43, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 17, 17, 12, 12, 14, 14, 20, 20, 32, 43, 43, 43, 43, 43, 43, 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: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/400 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)c1cccn1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338965195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338965195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338965195 none COCCN(CCNC(=O)c1cccn1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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: [25, 16, 11, 9, 2, 9, 14, 20, 32, 32, 32, 43, 43, 43, 43, 43, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 16, 16, 11, 11, 14, 14, 20, 20, 32, 43, 43, 43, 43, 43, 43, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338965195 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195 Building ZINC001338965195 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338965195 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 399) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)c1cccn1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338965195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338965195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338965195 none COCCN(CCNC(=O)c1cccn1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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: [27, 17, 12, 9, 2, 9, 14, 20, 32, 32, 32, 43, 43, 43, 43, 43, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 17, 17, 12, 12, 14, 14, 20, 20, 32, 43, 43, 43, 43, 43, 43, 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: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 400) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)c1cccn1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338965195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338965195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338965195 none COCCN(CCNC(=O)c1cccn1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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: [25, 16, 11, 9, 2, 9, 14, 20, 32, 32, 32, 43, 43, 43, 43, 43, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 16, 16, 11, 11, 14, 14, 20, 20, 32, 43, 43, 43, 43, 43, 43, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338965195 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965195 Building ZINC001338965495 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338965495 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/401 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1cc[nH]n1) `ZINC001338965495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338965495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338965495 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1cc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 13, 13, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 15, 15, 26, 38, 38, 38, 38, 38, 27, 27, 27, 19, 19, 13, 13, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 38, 38] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/2379/xbv-8058097.48/working/building/ZINC001338965495 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/402 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1cc[nH]n1) `ZINC001338965495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338965495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338965495 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1cc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 13, 13, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 15, 15, 26, 38, 38, 38, 38, 38, 27, 27, 27, 19, 19, 13, 13, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 38, 38] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/2379/xbv-8058097.48/working/building/ZINC001338965495 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338965495 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495 Building ZINC001338965495 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338965495 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 401) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1cc[nH]n1) `ZINC001338965495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338965495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338965495 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1cc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 13, 13, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 15, 15, 26, 38, 38, 38, 38, 38, 27, 27, 27, 19, 19, 13, 13, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 38, 38] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/2379/xbv-8058097.48/working/building/ZINC001338965495 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 402) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1cc[nH]n1) `ZINC001338965495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338965495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001338965495 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1cc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 13, 13, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 15, 15, 26, 38, 38, 38, 38, 38, 27, 27, 27, 19, 19, 13, 13, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 38, 38] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/2379/xbv-8058097.48/working/building/ZINC001338965495 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338965495 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965495 Building ZINC001338965833 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338965833 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/403 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnnc1) `ZINC001338965833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338965833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001338965833 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 33, 21, 17, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 30, 30, 30, 30, 30, 35, 35, 35, 33, 33, 21, 21, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/404 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/404' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnnc1) `ZINC001338965833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338965833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001338965833 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 33, 21, 17, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 30, 30, 30, 30, 30, 35, 35, 35, 33, 33, 21, 21, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338965833 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833 Building ZINC001338965833 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338965833 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 403) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnnc1) `ZINC001338965833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338965833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001338965833 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 33, 21, 17, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 30, 30, 30, 30, 30, 35, 35, 35, 33, 33, 21, 21, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 404) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnnc1) `ZINC001338965833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338965833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001338965833 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 33, 21, 17, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 30, 30, 30, 30, 30, 35, 35, 35, 33, 33, 21, 21, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338965833 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338965833 Building ZINC001338966075 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966075 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/405 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccon1) `ZINC001338966075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001338966075 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 39, 26, 19, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 33, 33, 39, 39, 39, 39, 44, 44, 44, 39, 39, 27, 27, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/406 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/406' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccon1) `ZINC001338966075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001338966075 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 38, 25, 18, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 32, 32, 41, 41, 41, 41, 43, 43, 43, 38, 38, 26, 26, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966075 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075 Building ZINC001338966075 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966075 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 405) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccon1) `ZINC001338966075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001338966075 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 39, 26, 19, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 33, 33, 39, 39, 39, 39, 44, 44, 44, 39, 39, 27, 27, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 406) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccon1) `ZINC001338966075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001338966075 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 38, 25, 18, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 32, 32, 41, 41, 41, 41, 43, 43, 43, 38, 38, 26, 26, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966075 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966075 Building ZINC001338966094 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966094 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/407 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1nonc1C) `ZINC001338966094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001338966094 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1nonc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 8, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [37, 29, 21, 15, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 26, 26, 38, 38, 38, 38, 38, 37, 37, 37, 29, 29, 22, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/408 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1nonc1C) `ZINC001338966094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001338966094 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1nonc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 8, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [38, 30, 21, 15, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 27, 27, 40, 40, 40, 40, 40, 38, 38, 38, 30, 30, 22, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966094 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094 Building ZINC001338966094 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966094 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 407) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1nonc1C) `ZINC001338966094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001338966094 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1nonc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 8, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [37, 29, 21, 15, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 26, 26, 38, 38, 38, 38, 38, 37, 37, 37, 29, 29, 22, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 408) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1nonc1C) `ZINC001338966094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001338966094 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1nonc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 8, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [38, 30, 21, 15, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 27, 27, 40, 40, 40, 40, 40, 38, 38, 38, 30, 30, 22, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966094 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966094 Building ZINC001338966125 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966125 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/409 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1CCOCC1) `ZINC001338966125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338966125 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 20, 15, 10, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 18, 26, 26, 26, 26, 26, 26, 36, 36, 36, 31, 31, 22, 22, 10, 10, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/410 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/410' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1CCOCC1) `ZINC001338966125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338966125 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 20, 15, 10, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 18, 26, 26, 26, 26, 26, 26, 36, 36, 36, 31, 31, 22, 22, 10, 10, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966125 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125 Building ZINC001338966125 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966125 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 409) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1CCOCC1) `ZINC001338966125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338966125 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 20, 15, 10, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 18, 26, 26, 26, 26, 26, 26, 36, 36, 36, 31, 31, 22, 22, 10, 10, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 410) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1CCOCC1) `ZINC001338966125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338966125 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 20, 15, 10, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 18, 26, 26, 26, 26, 26, 26, 36, 36, 36, 31, 31, 22, 22, 10, 10, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966125 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966125 Building ZINC001338966165 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966165 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/411 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cscn1) `ZINC001338966165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001338966165 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cscn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 18, 15, 8, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 25, 25, 35, 35, 35, 35, 30, 30, 30, 30, 30, 18, 18, 8, 8, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/412 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/412' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cscn1) `ZINC001338966165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001338966165 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cscn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 18, 14, 7, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 25, 25, 34, 34, 34, 34, 31, 31, 31, 31, 31, 18, 18, 7, 7, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966165 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165 Building ZINC001338966165 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966165 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 411) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cscn1) `ZINC001338966165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001338966165 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cscn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 18, 15, 8, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 25, 25, 35, 35, 35, 35, 30, 30, 30, 30, 30, 18, 18, 8, 8, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 412) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cscn1) `ZINC001338966165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001338966165 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cscn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 18, 14, 7, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 25, 25, 34, 34, 34, 34, 31, 31, 31, 31, 31, 18, 18, 7, 7, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966165 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966165 Building ZINC001338966291 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966291 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/413 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CCOC1) `ZINC001338966291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338966291 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 48, 31, 18, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 21, 23, 23, 23, 23, 23, 23, 49, 49, 49, 48, 48, 31, 31, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 254 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/414 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/414' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CCOC1) `ZINC001338966291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338966291 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 29, 18, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 23, 25, 25, 25, 25, 25, 25, 48, 48, 48, 46, 46, 29, 29, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 245 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966291 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291 Building ZINC001338966291 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966291 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 413) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CCOC1) `ZINC001338966291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338966291 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 48, 31, 18, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 21, 23, 23, 23, 23, 23, 23, 49, 49, 49, 48, 48, 31, 31, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 254 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 414) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CCOC1) `ZINC001338966291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338966291 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 29, 18, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 23, 25, 25, 25, 25, 25, 25, 48, 48, 48, 46, 46, 29, 29, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 245 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966291 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966291 Building ZINC001338966292 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966292 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/415 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CCOC1) `ZINC001338966292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338966292 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 29, 17, 11, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 26, 26, 26, 26, 26, 26, 49, 49, 49, 44, 44, 29, 29, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 240 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/416 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CCOC1) `ZINC001338966292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338966292 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 30, 16, 11, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 20, 26, 26, 26, 26, 26, 26, 49, 49, 49, 44, 44, 30, 30, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 247 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966292 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292 Building ZINC001338966292 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966292 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 415) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CCOC1) `ZINC001338966292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338966292 none COCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 29, 17, 11, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 26, 26, 26, 26, 26, 26, 49, 49, 49, 44, 44, 29, 29, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 240 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 416) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CCOC1) `ZINC001338966292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001338966292 none COCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 30, 16, 11, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 20, 26, 26, 26, 26, 26, 26, 49, 49, 49, 44, 44, 30, 30, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 247 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966292 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966292 Building ZINC001338966487 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966487 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/417 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)C1=COCCC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338966487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338966487 none COCCN(CCNC(=O)C1=COCCC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 5, 2, 5, 9, 13, 19, 19, 19, 39, 39, 39, 39, 39, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 8, 8, 6, 6, 9, 9, 13, 13, 19, 39, 39, 39, 39, 39, 39, 39, 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/418 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)C1=COCCC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338966487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338966487 none COCCN(CCNC(=O)C1=COCCC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 5, 2, 5, 8, 12, 17, 17, 17, 45, 45, 45, 45, 45, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 8, 8, 6, 6, 8, 8, 12, 12, 17, 45, 45, 45, 45, 45, 45, 45, 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966487 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487 Building ZINC001338966487 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338966487 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 417) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)C1=COCCC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338966487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338966487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338966487 none COCCN(CCNC(=O)C1=COCCC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 5, 2, 5, 9, 13, 19, 19, 19, 39, 39, 39, 39, 39, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 8, 8, 6, 6, 9, 9, 13, 13, 19, 39, 39, 39, 39, 39, 39, 39, 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 418) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)C1=COCCC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338966487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338966487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001338966487 none COCCN(CCNC(=O)C1=COCCC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 5, 2, 5, 8, 12, 17, 17, 17, 45, 45, 45, 45, 45, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 8, 8, 6, 6, 8, 8, 12, 12, 17, 45, 45, 45, 45, 45, 45, 45, 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338966487 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338966487 Building ZINC001338979774 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338979774 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/419 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)c1n[nH]cc1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338979774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338979774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338979774 none COCCN(CCNC(=O)c1n[nH]cc1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 9, 9, 3, 9, 15, 18, 36, 36, 36, 43, 43, 43, 43, 43, 43, 1, 3, 1, 1, 1, 1, 1, 1, 19, 19, 19, 13, 13, 9, 9, 15, 15, 18, 18, 36, 43, 43, 43, 43, 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: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/420 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)c1n[nH]cc1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338979774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338979774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338979774 none COCCN(CCNC(=O)c1n[nH]cc1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 9, 9, 3, 9, 15, 18, 36, 36, 36, 44, 44, 44, 44, 44, 44, 1, 3, 1, 1, 1, 1, 1, 1, 18, 18, 18, 13, 13, 9, 9, 15, 15, 18, 18, 36, 44, 44, 44, 44, 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: 167 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338979774 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774 Building ZINC001338979774 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338979774 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 419) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)c1n[nH]cc1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338979774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338979774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338979774 none COCCN(CCNC(=O)c1n[nH]cc1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 9, 9, 3, 9, 15, 18, 36, 36, 36, 43, 43, 43, 43, 43, 43, 1, 3, 1, 1, 1, 1, 1, 1, 19, 19, 19, 13, 13, 9, 9, 15, 15, 18, 18, 36, 43, 43, 43, 43, 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: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 420) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)c1n[nH]cc1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338979774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338979774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338979774 none COCCN(CCNC(=O)c1n[nH]cc1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 9, 9, 3, 9, 15, 18, 36, 36, 36, 44, 44, 44, 44, 44, 44, 1, 3, 1, 1, 1, 1, 1, 1, 18, 18, 18, 13, 13, 9, 9, 15, 15, 18, 18, 36, 44, 44, 44, 44, 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: 167 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338979774 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338979774 Building ZINC001338980945 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338980945 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/421 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 7, 4, 2, 4, 6, 9, 13, 13, 13, 35, 35, 35, 35, 35, 35, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 11, 11, 7, 7, 6, 6, 9, 9, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/422 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 10, 10, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/423 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/423' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 7, 4, 2, 4, 6, 9, 13, 13, 13, 35, 35, 35, 35, 35, 35, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 11, 11, 7, 7, 6, 6, 9, 9, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/424 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/424' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 10, 10, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338980945 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 Building ZINC001338980945 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338980945 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 421) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 7, 4, 2, 4, 6, 9, 13, 13, 13, 35, 35, 35, 35, 35, 35, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 11, 11, 7, 7, 6, 6, 9, 9, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 422) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 10, 10, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 423) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 7, 4, 2, 4, 6, 9, 13, 13, 13, 35, 35, 35, 35, 35, 35, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 11, 11, 7, 7, 6, 6, 9, 9, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 424) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 10, 10, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338980945 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 Building ZINC001338980945 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338980945 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 421) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 7, 4, 2, 4, 6, 9, 13, 13, 13, 35, 35, 35, 35, 35, 35, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 11, 11, 7, 7, 6, 6, 9, 9, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 422) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 10, 10, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 423) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 7, 4, 2, 4, 6, 9, 13, 13, 13, 35, 35, 35, 35, 35, 35, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 11, 11, 7, 7, 6, 6, 9, 9, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 424) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 10, 10, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338980945 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 Building ZINC001338980945 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338980945 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 421) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 7, 4, 2, 4, 6, 9, 13, 13, 13, 35, 35, 35, 35, 35, 35, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 11, 11, 7, 7, 6, 6, 9, 9, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 422) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 10, 10, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 423) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 7, 4, 2, 4, 6, 9, 13, 13, 13, 35, 35, 35, 35, 35, 35, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 11, 11, 7, 7, 6, 6, 9, 9, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 424) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980945.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338980945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980945 none COCCN(CCNC(=O)[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 10, 10, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338980945 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980945 Building ZINC001338980946 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338980946 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/425 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/426 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/426' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 2, 4, 4, 5, 9, 9, 9, 27, 27, 27, 27, 27, 27, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 9, 9, 6, 6, 4, 4, 5, 5, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/427 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/427' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/428 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/428' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 2, 4, 4, 5, 9, 9, 9, 27, 27, 27, 27, 27, 27, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 9, 9, 6, 6, 4, 4, 5, 5, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338980946 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 Building ZINC001338980946 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338980946 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 425) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 426) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 2, 4, 4, 5, 9, 9, 9, 27, 27, 27, 27, 27, 27, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 9, 9, 6, 6, 4, 4, 5, 5, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 427) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 428) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 2, 4, 4, 5, 9, 9, 9, 27, 27, 27, 27, 27, 27, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 9, 9, 6, 6, 4, 4, 5, 5, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338980946 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 Building ZINC001338980946 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338980946 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 425) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 426) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 2, 4, 4, 5, 9, 9, 9, 27, 27, 27, 27, 27, 27, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 9, 9, 6, 6, 4, 4, 5, 5, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 427) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 428) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 2, 4, 4, 5, 9, 9, 9, 27, 27, 27, 27, 27, 27, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 9, 9, 6, 6, 4, 4, 5, 5, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338980946 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 Building ZINC001338980946 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001338980946 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 425) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 426) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 2, 4, 4, 5, 9, 9, 9, 27, 27, 27, 27, 27, 27, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 9, 9, 6, 6, 4, 4, 5, 5, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 427) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 7, 4, 2, 4, 6, 9, 14, 14, 14, 36, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 7, 7, 6, 6, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 428) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338980946.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001338980946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338980946 none COCCN(CCNC(=O)[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 2, 4, 4, 5, 9, 9, 9, 27, 27, 27, 27, 27, 27, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 9, 9, 6, 6, 4, 4, 5, 5, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338980946 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338980946 Building ZINC001338983427 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338983427 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/429 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@]12C[C@H]1COC2)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338983427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338983427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338983427 none COCCN(CCNC(=O)[C@]12C[C@H]1COC2)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 10, 10, 3, 10, 16, 18, 26, 26, 26, 47, 47, 47, 47, 47, 47, 1, 3, 1, 1, 1, 1, 1, 1, 19, 19, 19, 12, 12, 10, 10, 16, 16, 18, 18, 26, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/430 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCNC(=O)[C@]12C[C@H]1COC2)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338983427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338983427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338983427 none COCCN(CCNC(=O)[C@]12C[C@H]1COC2)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 9, 9, 3, 9, 15, 19, 30, 30, 30, 46, 46, 46, 46, 46, 46, 1, 3, 1, 1, 1, 1, 1, 1, 17, 17, 17, 13, 13, 9, 9, 15, 15, 19, 19, 30, 46, 46, 46, 46, 46, 46, 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: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338983427 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427 Building ZINC001338983427 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338983427 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 429) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@]12C[C@H]1COC2)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001338983427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338983427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338983427 none COCCN(CCNC(=O)[C@]12C[C@H]1COC2)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 10, 10, 3, 10, 16, 18, 26, 26, 26, 47, 47, 47, 47, 47, 47, 1, 3, 1, 1, 1, 1, 1, 1, 19, 19, 19, 12, 12, 10, 10, 16, 16, 18, 18, 26, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 430) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCN(CCNC(=O)[C@]12C[C@H]1COC2)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001338983427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338983427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001338983427 none COCCN(CCNC(=O)[C@]12C[C@H]1COC2)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 9, 9, 3, 9, 15, 19, 30, 30, 30, 46, 46, 46, 46, 46, 46, 1, 3, 1, 1, 1, 1, 1, 1, 17, 17, 17, 13, 13, 9, 9, 15, 15, 19, 19, 30, 46, 46, 46, 46, 46, 46, 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: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338983427 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338983427 Building ZINC001338998982 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338998982 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/431 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@H]2C[S@@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338998982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998982 none CCn1cc([C@H]2C[S@@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 30, 30, 30, 30, 30, 17, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 17] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/432 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/432' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@H]2C[S@@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338998982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998982 none CCn1cc([C@H]2C[S@@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 19, 19, 19, 9, 9, 9, 9, 9, 9, 9, 9, 8, 3, 8, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 31, 31, 31, 31, 31, 19, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 19] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338998982 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982 Building ZINC001338998982 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338998982 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 431) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc([C@H]2C[S@@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338998982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998982 none CCn1cc([C@H]2C[S@@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 30, 30, 30, 30, 30, 17, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 17] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 432) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc([C@H]2C[S@@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338998982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998982 none CCn1cc([C@H]2C[S@@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 19, 19, 19, 9, 9, 9, 9, 9, 9, 9, 9, 8, 3, 8, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 31, 31, 31, 31, 31, 19, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 19] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338998982 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998982 Building ZINC001338998983 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338998983 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/433 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@H]2C[S@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338998983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998983 none CCn1cc([C@@H]2C[S@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 30, 30, 30, 30, 30, 18, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 18] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/434 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/434' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@H]2C[S@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338998983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998983 none CCn1cc([C@@H]2C[S@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 9, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 30, 30, 30, 30, 30, 19, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 19] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338998983 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983 Building ZINC001338998983 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338998983 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 433) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc([C@@H]2C[S@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338998983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998983 none CCn1cc([C@@H]2C[S@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 30, 30, 30, 30, 30, 18, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 18] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 434) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc([C@@H]2C[S@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338998983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998983 none CCn1cc([C@@H]2C[S@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 9, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 30, 30, 30, 30, 30, 19, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 19] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338998983 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998983 Building ZINC001338998984 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338998984 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/435 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@H]2C[S@@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338998984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998984 none CCn1cc([C@@H]2C[S@@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 31, 31, 31, 31, 31, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/436 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@H]2C[S@@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338998984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998984 none CCn1cc([C@@H]2C[S@@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 28, 28, 28, 28, 28, 16, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338998984 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984 Building ZINC001338998984 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338998984 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 435) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc([C@@H]2C[S@@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338998984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998984 none CCn1cc([C@@H]2C[S@@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 31, 31, 31, 31, 31, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 436) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc([C@@H]2C[S@@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338998984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998984 none CCn1cc([C@@H]2C[S@@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 28, 28, 28, 28, 28, 16, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338998984 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998984 Building ZINC001338998985 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338998985 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/437 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@H]2C[S@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338998985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998985 none CCn1cc([C@H]2C[S@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 32, 32, 32, 32, 32, 17, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 17] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/438 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/438' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@H]2C[S@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338998985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998985 none CCn1cc([C@H]2C[S@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 18, 18, 31, 31, 31, 31, 31, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338998985 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985 Building ZINC001338998985 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001338998985 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 437) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc([C@H]2C[S@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001338998985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998985 none CCn1cc([C@H]2C[S@](=O)CCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 32, 32, 32, 32, 32, 17, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 17] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 438) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1cc([C@H]2C[S@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1) `ZINC001338998985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001338998985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001338998985 none CCn1cc([C@H]2C[S@](=O)CCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 5, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 18, 18, 31, 31, 31, 31, 31, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001338998985 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001338998985 Building ZINC001339031975 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339031975 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/439 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)CNC(N)=O)CC1) `ZINC001339031975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339031975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339031975 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)CNC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 26, 26, 26, 26, 36, 36, 46, 50, 50, 50, 26, 26, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 46, 46, 50, 50, 50, 26, 26, 26, 26] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/440 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)CNC(N)=O)CC1) `ZINC001339031975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339031975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339031975 none C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)CNC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 24, 24, 24, 24, 37, 37, 45, 50, 50, 50, 24, 24, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 45, 45, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339031975 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975 Building ZINC001339031975 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339031975 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 439) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)CNC(N)=O)CC1) `ZINC001339031975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339031975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339031975 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)CNC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 26, 26, 26, 26, 36, 36, 46, 50, 50, 50, 26, 26, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 46, 46, 50, 50, 50, 26, 26, 26, 26] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 440) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)CNC(N)=O)CC1) `ZINC001339031975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339031975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339031975 none C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)CNC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 24, 24, 24, 24, 37, 37, 45, 50, 50, 50, 24, 24, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 45, 45, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339031975 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339031975 Building ZINC001339033327 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339033327 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/441 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CCC([C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339033327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339033327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001339033327 none CNC(=O)CC(=O)N1CCC([C@@H](C)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 25, 14, 25, 14, 14, 14, 6, 2, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 40, 40, 14, 14, 14, 14, 14, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 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: 187 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/442 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/442' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CCC([C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339033327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339033327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001339033327 none CNC(=O)CC(=O)N1CCC([C@@H](C)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 22, 14, 22, 14, 14, 14, 8, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 40, 40, 14, 14, 14, 14, 14, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 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: 198 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339033327 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327 Building ZINC001339033327 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339033327 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 441) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1CCC([C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339033327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339033327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001339033327 none CNC(=O)CC(=O)N1CCC([C@@H](C)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 25, 14, 25, 14, 14, 14, 6, 2, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 40, 40, 14, 14, 14, 14, 14, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 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: 187 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 442) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1CCC([C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339033327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339033327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001339033327 none CNC(=O)CC(=O)N1CCC([C@@H](C)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 22, 14, 22, 14, 14, 14, 8, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 40, 40, 14, 14, 14, 14, 14, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 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: 198 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339033327 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339033327 Building ZINC001339082426 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339082426 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/443 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)c2cnn(C)n2)CC1) `ZINC001339082426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339082426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339082426 none C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)c2cnn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 23, 23, 23, 23, 48, 48, 50, 50, 50, 50, 50, 23, 23, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/444 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/444' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)c2cnn(C)n2)CC1) `ZINC001339082426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339082426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339082426 none C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)c2cnn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 46, 46, 50, 50, 50, 50, 50, 23, 23, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339082426 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426 Building ZINC001339082426 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339082426 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 443) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)c2cnn(C)n2)CC1) `ZINC001339082426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339082426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339082426 none C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)c2cnn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 23, 23, 23, 23, 48, 48, 50, 50, 50, 50, 50, 23, 23, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 444) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)c2cnn(C)n2)CC1) `ZINC001339082426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339082426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339082426 none C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)c2cnn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 46, 46, 50, 50, 50, 50, 50, 23, 23, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339082426 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339082426 Building ZINC001339136677 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339136677 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/445 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/446 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/446' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/447 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/447' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/448 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/448' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339136677 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 Building ZINC001339136677 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339136677 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 445) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 446) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 447) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 448) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339136677 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 Building ZINC001339136677 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339136677 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 445) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 446) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 447) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 448) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339136677 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 Building ZINC001339136677 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339136677 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 445) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 446) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 447) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 448) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339136677.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339136677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339136677 none CN(C(=O)CCn1cccn1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 27, 27, 36, 40, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 36, 36, 40, 40, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339136677 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339136677 Building ZINC001339141907 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339141907 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/449 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/450 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/450' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/451 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/451' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/452 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/452' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339141907 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 Building ZINC001339141907 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339141907 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 449) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 450) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 451) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 452) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339141907 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 Building ZINC001339141907 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339141907 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 449) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 450) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 451) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 452) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339141907 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 Building ZINC001339141907 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339141907 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 449) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 450) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 451) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 452) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339141907.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339141907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339141907 none CN(C(=O)CNC(=O)C1CC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 25, 30, 30, 30, 50, 50, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 25, 25, 30, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339141907 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339141907 Building ZINC001339152874 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339152874 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/453 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 30, 13, 7, 13, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 30, 30, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/454 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/454' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 30, 13, 7, 13, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 30, 30, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/455 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/455' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 30, 13, 7, 13, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 30, 30, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/456 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/456' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 29, 12, 7, 12, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 29, 29, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339152874 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 Building ZINC001339152874 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339152874 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 453) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 30, 13, 7, 13, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 30, 30, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 454) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 30, 13, 7, 13, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 30, 30, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 455) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 30, 13, 7, 13, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 30, 30, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 456) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 29, 12, 7, 12, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 29, 29, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339152874 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 Building ZINC001339152874 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339152874 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 453) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 30, 13, 7, 13, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 30, 30, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 454) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 30, 13, 7, 13, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 30, 30, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 455) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 30, 13, 7, 13, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 30, 30, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 456) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 29, 12, 7, 12, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 29, 29, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339152874 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 Building ZINC001339152874 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339152874 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 453) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 30, 13, 7, 13, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 30, 30, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 454) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 30, 13, 7, 13, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 30, 30, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 455) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 30, 13, 7, 13, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 30, 30, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 456) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339152874.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339152874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339152874 none COCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 29, 12, 7, 12, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 48, 48, 29, 29, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/2379/xbv-8058097.48/working/building/ZINC001339152874 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339152874 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339152874 Building ZINC001339160098 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339160098 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/457 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)CC1CCOCC1) `ZINC001339160098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339160098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339160098 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 35, 32, 36, 35, 48, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 36, 36, 108, 40, 40, 48, 48, 48, 48, 48, 48, 48, 48, 48] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 321 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/458 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/458' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](CO)CC1CCOCC1) `ZINC001339160098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339160098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339160098 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](CO)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 29, 27, 31, 29, 45, 45, 45, 45, 45, 45, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 31, 31, 93, 37, 37, 45, 45, 45, 45, 45, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 286 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339160098 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098 Building ZINC001339160098 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339160098 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 457) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)CC1CCOCC1) `ZINC001339160098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339160098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339160098 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 35, 32, 36, 35, 48, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 36, 36, 108, 40, 40, 48, 48, 48, 48, 48, 48, 48, 48, 48] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 321 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 458) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](CO)CC1CCOCC1) `ZINC001339160098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339160098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339160098 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](CO)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 29, 27, 31, 29, 45, 45, 45, 45, 45, 45, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 31, 31, 93, 37, 37, 45, 45, 45, 45, 45, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 286 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339160098 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160098 Building ZINC001339160099 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339160099 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/459 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](CO)CC1CCOCC1) `ZINC001339160099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339160099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339160099 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](CO)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 28, 25, 30, 28, 44, 44, 44, 44, 44, 44, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 30, 30, 90, 36, 36, 44, 44, 44, 44, 44, 44, 44, 44, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 284 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/460 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](CO)CC1CCOCC1) `ZINC001339160099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339160099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339160099 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](CO)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 34, 32, 35, 34, 46, 46, 46, 46, 46, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 35, 35, 105, 39, 39, 46, 46, 46, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339160099 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099 Building ZINC001339160099 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339160099 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 459) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](CO)CC1CCOCC1) `ZINC001339160099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339160099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339160099 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](CO)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 28, 25, 30, 28, 44, 44, 44, 44, 44, 44, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 30, 30, 90, 36, 36, 44, 44, 44, 44, 44, 44, 44, 44, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 284 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 460) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](CO)CC1CCOCC1) `ZINC001339160099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339160099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339160099 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](CO)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 34, 32, 35, 34, 46, 46, 46, 46, 46, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 35, 35, 105, 39, 39, 46, 46, 46, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339160099 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339160099 Building ZINC001339163154 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163154 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/461 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 50, 32, 32, 11, 11, 11, 11, 3, 11, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/462 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/462' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 12, 12, 12, 12, 4, 12, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/463 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/463' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 12, 12, 12, 12, 4, 12, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/464 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/464' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 12, 12, 12, 12, 4, 12, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163154 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 Building ZINC001339163154 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163154 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 461) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 50, 32, 32, 11, 11, 11, 11, 3, 11, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 462) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 12, 12, 12, 12, 4, 12, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 463) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 12, 12, 12, 12, 4, 12, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 464) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 12, 12, 12, 12, 4, 12, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163154 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 Building ZINC001339163154 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163154 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 461) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 50, 32, 32, 11, 11, 11, 11, 3, 11, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 462) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 12, 12, 12, 12, 4, 12, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 463) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 12, 12, 12, 12, 4, 12, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 464) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 12, 12, 12, 12, 4, 12, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163154 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 Building ZINC001339163154 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163154 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 461) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 50, 32, 32, 11, 11, 11, 11, 3, 11, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 462) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 12, 12, 12, 12, 4, 12, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 463) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 12, 12, 12, 12, 4, 12, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 464) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163154.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163154 none CC(=O)NC(C)(C)C(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 12, 12, 12, 12, 4, 12, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163154 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163154 Building ZINC001339163201 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163201 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/465 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 15, 15, 15, 45, 47, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 45, 45, 47, 47, 50, 50, 50, 50, 5, 5] 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: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/466 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/466' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 48, 49, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 48, 48, 49, 49, 50, 50, 50, 50, 5, 5] 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: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/467 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/467' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 46, 48, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 46, 46, 48, 48, 50, 50, 50, 50, 5, 5] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/468 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/468' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 48, 49, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 48, 48, 49, 49, 50, 50, 50, 50, 5, 5] 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: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163201 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 Building ZINC001339163201 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163201 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 465) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 15, 15, 15, 45, 47, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 45, 45, 47, 47, 50, 50, 50, 50, 5, 5] 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: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 466) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 48, 49, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 48, 48, 49, 49, 50, 50, 50, 50, 5, 5] 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: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 467) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 46, 48, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 46, 46, 48, 48, 50, 50, 50, 50, 5, 5] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 468) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 48, 49, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 48, 48, 49, 49, 50, 50, 50, 50, 5, 5] 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: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163201 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 Building ZINC001339163201 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163201 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 465) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 15, 15, 15, 45, 47, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 45, 45, 47, 47, 50, 50, 50, 50, 5, 5] 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: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 466) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 48, 49, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 48, 48, 49, 49, 50, 50, 50, 50, 5, 5] 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: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 467) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 46, 48, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 46, 46, 48, 48, 50, 50, 50, 50, 5, 5] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 468) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 48, 49, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 48, 48, 49, 49, 50, 50, 50, 50, 5, 5] 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: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163201 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 Building ZINC001339163201 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163201 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 465) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 15, 15, 15, 45, 47, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 45, 45, 47, 47, 50, 50, 50, 50, 5, 5] 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: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 466) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 48, 49, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 48, 48, 49, 49, 50, 50, 50, 50, 5, 5] 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: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 467) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 46, 48, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 46, 46, 48, 48, 50, 50, 50, 50, 5, 5] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 468) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1) `ZINC001339163201.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339163201 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCc2cnn(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 48, 49, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 48, 48, 49, 49, 50, 50, 50, 50, 5, 5] 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: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163201 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163201 Building ZINC001339163325 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163325 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/469 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 23, 23, 23, 50, 50, 50, 50, 50, 50, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/470 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/470' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 21, 21, 21, 49, 50, 50, 50, 50, 50, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 49, 49, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/471 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/471' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 23, 23, 23, 50, 50, 50, 50, 50, 50, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/472 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/472' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 21, 21, 21, 49, 50, 50, 50, 50, 50, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 49, 49, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163325 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 Building ZINC001339163325 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163325 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 469) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 23, 23, 23, 50, 50, 50, 50, 50, 50, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 470) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 21, 21, 21, 49, 50, 50, 50, 50, 50, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 49, 49, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 471) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 23, 23, 23, 50, 50, 50, 50, 50, 50, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 472) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 21, 21, 21, 49, 50, 50, 50, 50, 50, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 49, 49, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163325 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 Building ZINC001339163325 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163325 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 469) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 23, 23, 23, 50, 50, 50, 50, 50, 50, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 470) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 21, 21, 21, 49, 50, 50, 50, 50, 50, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 49, 49, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 471) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 23, 23, 23, 50, 50, 50, 50, 50, 50, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 472) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 21, 21, 21, 49, 50, 50, 50, 50, 50, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 49, 49, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163325 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 Building ZINC001339163325 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163325 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 469) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 23, 23, 23, 50, 50, 50, 50, 50, 50, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 470) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 21, 21, 21, 49, 50, 50, 50, 50, 50, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 49, 49, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 471) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 23, 23, 23, 50, 50, 50, 50, 50, 50, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 472) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1) `ZINC001339163325.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163325 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 21, 21, 21, 49, 50, 50, 50, 50, 50, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 49, 49, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/2379/xbv-8058097.48/working/building/ZINC001339163325 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163325 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163325 Building ZINC001339163377 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163377 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/473 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/474 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/474' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/475 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/475' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/476 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/476' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163377 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 Building ZINC001339163377 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163377 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 473) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 474) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 475) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 476) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163377 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 Building ZINC001339163377 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163377 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 473) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 474) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 475) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 476) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163377 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 Building ZINC001339163377 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163377 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 473) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 474) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 475) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 476) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1) `ZINC001339163377.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163377 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)c2ccc(=O)n(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 8, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 50, 50, 50, 50, 50, 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: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163377 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163377 Building ZINC001339163552 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163552 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/477 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 16, 16, 16, 5, 5, 5, 5, 2, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 38, 38, 16, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/478 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 15, 15, 15, 5, 5, 5, 5, 2, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 39, 39, 15, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/479 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/479' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 14, 14, 14, 4, 4, 4, 4, 2, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 39, 39, 14, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/480 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/480' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 14, 14, 14, 4, 4, 4, 4, 2, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 39, 39, 14, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163552 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 Building ZINC001339163552 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163552 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 477) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 16, 16, 16, 5, 5, 5, 5, 2, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 38, 38, 16, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 478) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 15, 15, 15, 5, 5, 5, 5, 2, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 39, 39, 15, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 479) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 14, 14, 14, 4, 4, 4, 4, 2, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 39, 39, 14, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 480) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 14, 14, 14, 4, 4, 4, 4, 2, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 39, 39, 14, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163552 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 Building ZINC001339163552 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163552 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 477) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 16, 16, 16, 5, 5, 5, 5, 2, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 38, 38, 16, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 478) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 15, 15, 15, 5, 5, 5, 5, 2, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 39, 39, 15, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 479) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 14, 14, 14, 4, 4, 4, 4, 2, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 39, 39, 14, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 480) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 14, 14, 14, 4, 4, 4, 4, 2, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 39, 39, 14, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163552 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 Building ZINC001339163552 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163552 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 477) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 16, 16, 16, 5, 5, 5, 5, 2, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 38, 38, 16, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 478) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 15, 15, 15, 5, 5, 5, 5, 2, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 39, 39, 15, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 479) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 14, 14, 14, 4, 4, 4, 4, 2, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 39, 39, 14, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 480) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163552.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163552 none Cc1cncn1CC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 14, 14, 14, 4, 4, 4, 4, 2, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 39, 39, 14, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163552 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163552 Building ZINC001339163567 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163567 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/481 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 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: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/482 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/482' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 8, 27, 27, 33, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 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: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/483 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/483' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 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: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/484 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/484' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 8, 27, 27, 33, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 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: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163567 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 Building ZINC001339163567 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163567 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 481) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 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: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 482) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 8, 27, 27, 33, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 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: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 483) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 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: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 484) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 8, 27, 27, 33, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 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: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163567 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 Building ZINC001339163567 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163567 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 481) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 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: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 482) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 8, 27, 27, 33, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 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: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 483) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 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: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 484) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 8, 27, 27, 33, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 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: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163567 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 Building ZINC001339163567 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163567 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 481) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 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: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 482) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 8, 27, 27, 33, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 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: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 483) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 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: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 484) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001339163567.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339163567 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CCC(=O)N2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 8, 27, 27, 33, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 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: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163567 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163567 Building ZINC001339163588 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163588 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/485 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 25, 18, 12, 12, 12, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 18, 18, 12, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/486 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/486' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 27, 17, 13, 13, 13, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 17, 17, 13, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/487 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/487' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 25, 17, 11, 11, 11, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 17, 17, 11, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/488 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/488' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 18, 14, 14, 14, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 18, 18, 14, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163588 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 Building ZINC001339163588 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163588 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 485) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 25, 18, 12, 12, 12, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 18, 18, 12, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 486) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 27, 17, 13, 13, 13, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 17, 17, 13, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 487) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 25, 17, 11, 11, 11, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 17, 17, 11, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 488) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 18, 14, 14, 14, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 18, 18, 14, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163588 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 Building ZINC001339163588 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163588 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 485) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 25, 18, 12, 12, 12, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 18, 18, 12, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 486) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 27, 17, 13, 13, 13, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 17, 17, 13, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 487) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 25, 17, 11, 11, 11, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 17, 17, 11, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 488) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 18, 14, 14, 14, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 18, 18, 14, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163588 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 Building ZINC001339163588 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163588 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 485) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 25, 18, 12, 12, 12, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 18, 18, 12, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 486) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 27, 17, 13, 13, 13, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 17, 17, 13, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 487) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 25, 17, 11, 11, 11, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 17, 17, 11, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 488) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339163588.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339163588 none CN(C)CCOCC(=O)N[C@H]1C[C@@H](N(C)C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 18, 14, 14, 14, 6, 6, 6, 6, 2, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 18, 18, 14, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339163588 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339163588 Building ZINC001339170090 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339170090 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/489 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/490 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/490' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/491 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/491' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/492 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/492' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339170090 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 Building ZINC001339170090 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339170090 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 489) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 490) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 491) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 492) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339170090 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 Building ZINC001339170090 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339170090 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 489) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 490) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 491) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 492) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339170090 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 Building ZINC001339170090 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339170090 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 489) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 490) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 491) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 492) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339170090.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339170090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339170090 none CN(C(=O)CN1CCOCC1)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 27, 27, 46, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/2379/xbv-8058097.48/working/building/ZINC001339170090 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339170090 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339170090 Building ZINC001339198454 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339198454 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/493 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/494 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/494' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/495 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/495' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/496 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/496' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339198454 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 Building ZINC001339198454 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339198454 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 493) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 494) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 495) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 496) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339198454 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 Building ZINC001339198454 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339198454 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 493) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 494) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 495) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 496) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339198454 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 Building ZINC001339198454 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339198454 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 493) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 494) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 495) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 496) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339198454.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339198454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339198454 none Cc1ccnn1CC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 20, 36, 7, 20, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 47, 47, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339198454 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339198454 Building ZINC001339217925 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339217925 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/497 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 36, 20, 36, 11, 20, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 150, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/498 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 36, 20, 36, 11, 20, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 150, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/499 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/499' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 37, 20, 37, 10, 20, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 150, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/500 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/500' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 36, 20, 36, 11, 20, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 150, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339217925 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 Building ZINC001339217925 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339217925 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 497) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 36, 20, 36, 11, 20, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 150, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 498) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 36, 20, 36, 11, 20, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 150, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 499) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 37, 20, 37, 10, 20, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 150, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 500) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 36, 20, 36, 11, 20, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 150, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339217925 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 Building ZINC001339217925 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339217925 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 497) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 36, 20, 36, 11, 20, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 150, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 498) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 36, 20, 36, 11, 20, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 150, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 499) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 37, 20, 37, 10, 20, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 150, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 500) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 36, 20, 36, 11, 20, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 150, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339217925 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 Building ZINC001339217925 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339217925 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 497) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 36, 20, 36, 11, 20, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 150, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 498) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 36, 20, 36, 11, 20, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 150, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 499) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 37, 20, 37, 10, 20, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 150, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 500) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339217925.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339217925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339217925 none Cc1nc(O)[nH]c1C(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 4, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 36, 20, 36, 11, 20, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 150, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339217925 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339217925 Building ZINC001339226359 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339226359 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/501 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/502 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/502' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/503 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/503' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/504 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/504' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339226359 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 Building ZINC001339226359 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339226359 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 501) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 502) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 503) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 504) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339226359 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 Building ZINC001339226359 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339226359 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 501) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 502) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 503) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 504) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339226359 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 Building ZINC001339226359 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339226359 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 501) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 502) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 503) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 504) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339226359.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339226359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339226359 none CN(C(=O)CCCC(N)=O)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 12, 12, 24, 19, 39, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 24, 24, 26, 26, 36, 36, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339226359 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339226359 Building ZINC001339281428 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339281428 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/505 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@]2(CO)CCCC[C@@]2(CO)C1) `ZINC001339281428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339281428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339281428 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@]2(CO)CCCC[C@@]2(CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 10, 21, 21, 21, 35, 21, 21, 21, 21, 21, 21, 33, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 35, 35, 105, 21, 21, 21, 21, 21, 21, 21, 21, 33, 33, 99, 21, 21] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 387 number of broken/clashed sets: 301 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/506 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/506' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@]2(CO)CCCC[C@@]2(CO)C1) `ZINC001339281428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339281428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339281428 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@]2(CO)CCCC[C@@]2(CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 9, 19, 19, 19, 33, 19, 19, 19, 19, 19, 19, 33, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 33, 33, 99, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 99, 19, 19] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 384 number of broken/clashed sets: 290 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339281428 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428 Building ZINC001339281428 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339281428 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 505) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@]2(CO)CCCC[C@@]2(CO)C1) `ZINC001339281428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339281428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339281428 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@]2(CO)CCCC[C@@]2(CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 10, 21, 21, 21, 35, 21, 21, 21, 21, 21, 21, 33, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 35, 35, 105, 21, 21, 21, 21, 21, 21, 21, 21, 33, 33, 99, 21, 21] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 387 number of broken/clashed sets: 301 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 506) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@]2(CO)CCCC[C@@]2(CO)C1) `ZINC001339281428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339281428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339281428 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@]2(CO)CCCC[C@@]2(CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 9, 19, 19, 19, 33, 19, 19, 19, 19, 19, 19, 33, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 33, 33, 99, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 99, 19, 19] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 384 number of broken/clashed sets: 290 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339281428 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339281428 Building ZINC001339293784 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339293784 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/507 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 34, 18, 11, 8, 11, 6, 8, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 46, 46, 40, 40, 18, 18, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/508 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/508' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 33, 18, 11, 8, 11, 6, 8, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 46, 46, 40, 40, 18, 18, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/509 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/509' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 33, 17, 11, 8, 11, 6, 8, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 46, 46, 40, 40, 17, 17, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/510 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/510' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 33, 17, 10, 7, 10, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 46, 46, 40, 40, 17, 17, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339293784 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 Building ZINC001339293784 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339293784 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 507) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 34, 18, 11, 8, 11, 6, 8, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 46, 46, 40, 40, 18, 18, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 508) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 33, 18, 11, 8, 11, 6, 8, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 46, 46, 40, 40, 18, 18, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 509) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 33, 17, 11, 8, 11, 6, 8, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 46, 46, 40, 40, 17, 17, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 510) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 33, 17, 10, 7, 10, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 46, 46, 40, 40, 17, 17, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339293784 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 Building ZINC001339293784 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339293784 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 507) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 34, 18, 11, 8, 11, 6, 8, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 46, 46, 40, 40, 18, 18, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 508) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 33, 18, 11, 8, 11, 6, 8, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 46, 46, 40, 40, 18, 18, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 509) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 33, 17, 11, 8, 11, 6, 8, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 46, 46, 40, 40, 17, 17, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 510) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 33, 17, 10, 7, 10, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 46, 46, 40, 40, 17, 17, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339293784 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 Building ZINC001339293784 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339293784 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 507) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 34, 18, 11, 8, 11, 6, 8, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 46, 46, 40, 40, 18, 18, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 508) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 33, 18, 11, 8, 11, 6, 8, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 46, 46, 40, 40, 18, 18, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 509) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 33, 17, 11, 8, 11, 6, 8, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 46, 46, 40, 40, 17, 17, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 510) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339293784.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339293784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001339293784 none COCCCOCC(=O)N(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 33, 17, 10, 7, 10, 5, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 46, 46, 40, 40, 17, 17, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339293784 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339293784 Building ZINC001339371756 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339371756 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/511 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCn2cncn2)CC1) `ZINC001339371756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339371756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339371756 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCn2cncn2)CC1 NO_LONG_NAME 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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 7, 7, 7, 7, 11, 17, 17, 17, 42, 44, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 17, 42, 42, 44, 44, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/512 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/512' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCn2cncn2)CC1) `ZINC001339371756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339371756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339371756 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCn2cncn2)CC1 NO_LONG_NAME 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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 9, 15, 15, 15, 43, 45, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 15, 43, 43, 45, 45, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339371756 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756 Building ZINC001339371756 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339371756 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 511) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCn2cncn2)CC1) `ZINC001339371756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339371756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339371756 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCn2cncn2)CC1 NO_LONG_NAME 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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 7, 7, 7, 7, 11, 17, 17, 17, 42, 44, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 17, 42, 42, 44, 44, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 512) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCn2cncn2)CC1) `ZINC001339371756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339371756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339371756 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCn2cncn2)CC1 NO_LONG_NAME 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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 9, 15, 15, 15, 43, 45, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 15, 43, 43, 45, 45, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339371756 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339371756 Building ZINC001339399785 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339399785 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/513 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1) `ZINC001339399785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339399785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399785 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 22, 35, 10, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 22, 23, 23, 23, 23, 23, 35, 35, 35, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/514 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/514' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1) `ZINC001339399785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339399785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399785 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 21, 32, 10, 21, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 21, 23, 23, 23, 23, 23, 32, 32, 32, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339399785 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785 Building ZINC001339399785 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339399785 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 513) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1) `ZINC001339399785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339399785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399785 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 22, 35, 10, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 22, 23, 23, 23, 23, 23, 35, 35, 35, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 514) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1) `ZINC001339399785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339399785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399785 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 21, 32, 10, 21, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 21, 23, 23, 23, 23, 23, 32, 32, 32, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339399785 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399785 Building ZINC001339399886 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339399886 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/515 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1) `ZINC001339399886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339399886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399886 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 22, 32, 10, 22, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 22, 25, 25, 25, 25, 25, 32, 32, 32, 10, 10, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/516 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1) `ZINC001339399886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339399886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399886 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 22, 36, 10, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 22, 24, 24, 24, 24, 24, 36, 36, 36, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339399886 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886 Building ZINC001339399886 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339399886 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 515) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1) `ZINC001339399886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339399886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399886 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 22, 32, 10, 22, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 22, 25, 25, 25, 25, 25, 32, 32, 32, 10, 10, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 516) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1) `ZINC001339399886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339399886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399886 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 22, 36, 10, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 22, 24, 24, 24, 24, 24, 36, 36, 36, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339399886 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399886 Building ZINC001339399887 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339399887 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/517 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1) `ZINC001339399887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339399887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399887 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 22, 34, 10, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 27, 27, 27, 27, 27, 34, 34, 34, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/518 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/518' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1) `ZINC001339399887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339399887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399887 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 23, 31, 9, 23, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 28, 28, 28, 28, 28, 31, 31, 31, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339399887 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887 Building ZINC001339399887 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339399887 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 517) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1) `ZINC001339399887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339399887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399887 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 22, 34, 10, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 27, 27, 27, 27, 27, 34, 34, 34, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 518) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1) `ZINC001339399887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339399887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399887 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 23, 31, 9, 23, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 28, 28, 28, 28, 28, 31, 31, 31, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339399887 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399887 Building ZINC001339399888 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339399888 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/519 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1) `ZINC001339399888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339399888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399888 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 23, 31, 9, 23, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 28, 28, 28, 28, 28, 31, 31, 31, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/520 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/520' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1) `ZINC001339399888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339399888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399888 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 22, 34, 10, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 27, 27, 27, 27, 27, 34, 34, 34, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339399888 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888 Building ZINC001339399888 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339399888 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 519) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1) `ZINC001339399888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339399888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399888 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 23, 31, 9, 23, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 28, 28, 28, 28, 28, 31, 31, 31, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 520) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1) `ZINC001339399888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339399888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001339399888 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 22, 34, 10, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 27, 27, 27, 27, 27, 34, 34, 34, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339399888 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339399888 Building ZINC001339420194 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339420194 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/521 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(=O)N2CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1) `ZINC001339420194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339420194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339420194 none Cc1nc(CC(=O)N2CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 33, 27, 33, 27, 27, 22, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 38, 38, 27, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 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: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/522 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(=O)N2CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1) `ZINC001339420194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339420194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339420194 none Cc1nc(CC(=O)N2CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 33, 27, 33, 27, 27, 21, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 38, 38, 27, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 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: 143 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339420194 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194 Building ZINC001339420194 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339420194 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 521) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(CC(=O)N2CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1) `ZINC001339420194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339420194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339420194 none Cc1nc(CC(=O)N2CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 33, 27, 33, 27, 27, 22, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 38, 38, 27, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 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: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 522) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(CC(=O)N2CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1) `ZINC001339420194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339420194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339420194 none Cc1nc(CC(=O)N2CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 33, 27, 33, 27, 27, 21, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 38, 38, 27, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 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: 143 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339420194 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420194 Building ZINC001339420702 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339420702 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/523 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N2CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)cn1) `ZINC001339420702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339420702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339420702 none Cn1cc(CC(=O)N2CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 31, 31, 31, 31, 31, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50, 50, 50, 50, 50, 42, 42, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 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, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/524 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N2CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)cn1) `ZINC001339420702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339420702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339420702 none Cn1cc(CC(=O)N2CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 31, 31, 31, 31, 31, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50, 50, 50, 50, 50, 42, 42, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 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, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339420702 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702 Building ZINC001339420702 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339420702 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 523) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(CC(=O)N2CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)cn1) `ZINC001339420702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339420702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339420702 none Cn1cc(CC(=O)N2CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 31, 31, 31, 31, 31, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50, 50, 50, 50, 50, 42, 42, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 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, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 524) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc(CC(=O)N2CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)cn1) `ZINC001339420702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339420702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339420702 none Cn1cc(CC(=O)N2CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 31, 31, 31, 31, 31, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50, 50, 50, 50, 50, 42, 42, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 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, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339420702 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339420702 Building ZINC001339421149 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339421149 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/525 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1CC(=O)N1CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339421149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339421149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001339421149 none Cc1nonc1CC(=O)N1CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 35, 35, 35, 35, 35, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 43, 43, 35, 35, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] 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, 45, 46, 47, 48]) total number of confs: 146 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/526 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/526' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1CC(=O)N1CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339421149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339421149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001339421149 none Cc1nonc1CC(=O)N1CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 36, 36, 36, 36, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 44, 44, 36, 36, 36, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] 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, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339421149 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149 Building ZINC001339421149 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339421149 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 525) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nonc1CC(=O)N1CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339421149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339421149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001339421149 none Cc1nonc1CC(=O)N1CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 35, 35, 35, 35, 35, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 43, 43, 35, 35, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] 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, 45, 46, 47, 48]) total number of confs: 146 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 526) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nonc1CC(=O)N1CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339421149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339421149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001339421149 none Cc1nonc1CC(=O)N1CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 36, 36, 36, 36, 36, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 44, 44, 36, 36, 36, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] 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, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339421149 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421149 Building ZINC001339421715 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339421715 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/527 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N2CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)c1) `ZINC001339421715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339421715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339421715 none Cn1cnc(C(=O)N2CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 50, 43, 43, 30, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/528 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/528' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N2CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)c1) `ZINC001339421715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339421715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339421715 none Cn1cnc(C(=O)N2CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 50, 42, 42, 30, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 42, 42, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339421715 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715 Building ZINC001339421715 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339421715 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 527) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cnc(C(=O)N2CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)c1) `ZINC001339421715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339421715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339421715 none Cn1cnc(C(=O)N2CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 50, 43, 43, 30, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 528) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cnc(C(=O)N2CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)c1) `ZINC001339421715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339421715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339421715 none Cn1cnc(C(=O)N2CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 50, 42, 42, 30, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 42, 42, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339421715 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339421715 Building ZINC001339422253 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339422253 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/529 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N1CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339422253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339422253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339422253 none CN(C)C(=O)CC(=O)N1CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 32, 32, 32, 32, 32, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50, 50, 43, 43, 32, 32, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/2379/xbv-8058097.48/working/building/ZINC001339422253 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/530 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/530' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N1CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339422253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339422253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339422253 none CN(C)C(=O)CC(=O)N1CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 32, 32, 32, 32, 32, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50, 50, 43, 43, 32, 32, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/2379/xbv-8058097.48/working/building/ZINC001339422253 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339422253 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253 Building ZINC001339422253 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339422253 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 529) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)C(=O)CC(=O)N1CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339422253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339422253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339422253 none CN(C)C(=O)CC(=O)N1CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 32, 32, 32, 32, 32, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50, 50, 43, 43, 32, 32, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/2379/xbv-8058097.48/working/building/ZINC001339422253 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 530) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CN(C)C(=O)CC(=O)N1CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339422253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339422253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339422253 none CN(C)C(=O)CC(=O)N1CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 32, 32, 32, 32, 32, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50, 50, 43, 43, 32, 32, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/2379/xbv-8058097.48/working/building/ZINC001339422253 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339422253 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422253 Building ZINC001339422288 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339422288 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/531 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2cc[nH]n2)CC1) `ZINC001339422288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339422288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339422288 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2cc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 26, 40, 40, 40, 45, 45, 50, 50, 50, 50, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 50, 50, 50, 50, 40, 40, 40, 40] 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: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/532 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2cc[nH]n2)CC1) `ZINC001339422288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339422288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339422288 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2cc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 27, 42, 42, 42, 47, 47, 50, 50, 50, 50, 50, 50, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 42, 42, 42, 50, 50, 50, 50, 42, 42, 42, 42] 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: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339422288 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288 Building ZINC001339422288 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339422288 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 531) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2cc[nH]n2)CC1) `ZINC001339422288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339422288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339422288 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2cc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 26, 40, 40, 40, 45, 45, 50, 50, 50, 50, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 50, 50, 50, 50, 40, 40, 40, 40] 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: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 532) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2cc[nH]n2)CC1) `ZINC001339422288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339422288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339422288 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2cc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 27, 42, 42, 42, 47, 47, 50, 50, 50, 50, 50, 50, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 42, 42, 42, 50, 50, 50, 50, 42, 42, 42, 42] 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: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339422288 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422288 Building ZINC001339422315 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339422315 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/533 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CC(=O)N1CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339422315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339422315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001339422315 none Cn1nccc1CC(=O)N1CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 38, 36, 38, 36, 36, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 41, 41, 36, 36, 36, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46] 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, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/534 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/534' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CC(=O)N1CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339422315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339422315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001339422315 none Cn1nccc1CC(=O)N1CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 39, 37, 39, 37, 37, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 50, 50, 50, 50, 50, 42, 42, 37, 37, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46] 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, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339422315 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315 Building ZINC001339422315 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339422315 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 533) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nccc1CC(=O)N1CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339422315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339422315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001339422315 none Cn1nccc1CC(=O)N1CC=C(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 38, 36, 38, 36, 36, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 41, 41, 36, 36, 36, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46] 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, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 534) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1nccc1CC(=O)N1CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001339422315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339422315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001339422315 none Cn1nccc1CC(=O)N1CC=C(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 39, 37, 39, 37, 37, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 50, 50, 50, 50, 50, 42, 42, 37, 37, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46] 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, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339422315 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339422315 Building ZINC001339423017 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339423017 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/535 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)C2(C(N)=O)CC2)CC1) `ZINC001339423017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339423017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339423017 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)C2(C(N)=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 31, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38] 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/536 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)C2(C(N)=O)CC2)CC1) `ZINC001339423017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339423017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339423017 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)C2(C(N)=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 31, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 36, 36, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36] 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: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339423017 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017 Building ZINC001339423017 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339423017 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 535) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)C2(C(N)=O)CC2)CC1) `ZINC001339423017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339423017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339423017 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)C2(C(N)=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 31, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38] 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 536) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)C2(C(N)=O)CC2)CC1) `ZINC001339423017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339423017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339423017 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)C2(C(N)=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 31, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 36, 36, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36] 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: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339423017 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339423017 Building ZINC001339424532 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339424532 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/537 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2nc[nH]n2)CC1) `ZINC001339424532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339424532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339424532 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 28, 28, 28, 32, 32, 34, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 28, 34, 34, 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: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/538 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2nc[nH]n2)CC1) `ZINC001339424532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339424532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339424532 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 28, 30, 30, 30, 32, 32, 34, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 30, 30, 30, 34, 34, 50, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339424532 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532 Building ZINC001339424532 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339424532 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 537) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2nc[nH]n2)CC1) `ZINC001339424532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339424532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339424532 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 28, 28, 28, 32, 32, 34, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 28, 34, 34, 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: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 538) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2nc[nH]n2)CC1) `ZINC001339424532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339424532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339424532 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)Cc2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 28, 30, 30, 30, 32, 32, 34, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 30, 30, 30, 34, 34, 50, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339424532 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339424532 Building ZINC001339427969 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339427969 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/539 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)Cc2cc[nH]n2)CC1) `ZINC001339427969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339427969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339427969 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)Cc2cc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 6, 6, 6, 15, 29, 29, 29, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 29, 50, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 221 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/540 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/540' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)Cc2cc[nH]n2)CC1) `ZINC001339427969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339427969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339427969 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)Cc2cc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 15, 28, 28, 28, 50, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 28, 50, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 224 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339427969 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969 Building ZINC001339427969 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339427969 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 539) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)Cc2cc[nH]n2)CC1) `ZINC001339427969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339427969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339427969 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)Cc2cc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 6, 6, 6, 15, 29, 29, 29, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 29, 50, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 221 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 540) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)Cc2cc[nH]n2)CC1) `ZINC001339427969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339427969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339427969 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)Cc2cc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 15, 28, 28, 28, 50, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 28, 50, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 224 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339427969 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339427969 Building ZINC001339438259 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339438259 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/541 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/541' -> `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(CNC(=O)CCc2nc[nH]n2)CC1) `ZINC001339438259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339438259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339438259 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCc2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 28, 28, 28, 32, 32, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 28, 32, 32, 32, 32, 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]) total number of confs: 148 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/542 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/542' -> `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(CNC(=O)CCc2nc[nH]n2)CC1) `ZINC001339438259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339438259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339438259 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCc2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 25, 25, 25, 30, 30, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 25, 30, 30, 30, 30, 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]) total number of confs: 149 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339438259 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259 Building ZINC001339438259 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339438259 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 541) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCc2nc[nH]n2)CC1) `ZINC001339438259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339438259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339438259 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCc2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 28, 28, 28, 32, 32, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 28, 32, 32, 32, 32, 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]) total number of confs: 148 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 542) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCc2nc[nH]n2)CC1) `ZINC001339438259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339438259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339438259 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CNC(=O)CCc2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 25, 25, 25, 30, 30, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 25, 30, 30, 30, 30, 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]) total number of confs: 149 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339438259 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339438259 Building ZINC001339659179 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659179 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/543 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339659179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659179 none CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 22, 20, 15, 20, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 38, 22, 22, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/544 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/544' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339659179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659179 none CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 22, 21, 17, 21, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 36, 22, 22, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 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, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659179 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179 Building ZINC001339659179 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659179 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 543) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339659179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659179 none CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 22, 20, 15, 20, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 38, 22, 22, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 544) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339659179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659179 none CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 22, 21, 17, 21, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 36, 22, 22, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 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, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659179 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659179 Building ZINC001339659180 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659180 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/545 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339659180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659180 none CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 22, 18, 22, 18, 18, 5, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 37, 23, 23, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/546 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/546' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339659180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659180 none CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 22, 20, 15, 20, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 39, 22, 22, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659180 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180 Building ZINC001339659180 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659180 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 545) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339659180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659180 none CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 22, 18, 22, 18, 18, 5, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 37, 23, 23, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 546) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339659180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659180 none CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 22, 20, 15, 20, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 39, 22, 22, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659180 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659180 Building ZINC001339659183 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659183 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/547 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339659183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659183 none CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 22, 15, 8, 15, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 32, 22, 22, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/548 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/548' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339659183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659183 none CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 18, 12, 18, 12, 12, 2, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 40, 28, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 205 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659183 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183 Building ZINC001339659183 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659183 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 547) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339659183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659183 none CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 22, 15, 8, 15, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 32, 22, 22, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 548) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339659183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659183 none CCC(=O)NCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 18, 12, 18, 12, 12, 2, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 40, 28, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 205 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659183 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659183 Building ZINC001339659185 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659185 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/549 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339659185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659185 none CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 29, 18, 12, 18, 12, 12, 2, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 40, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/550 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339659185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659185 none CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 41, 24, 18, 10, 18, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 41, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659185 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185 Building ZINC001339659185 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659185 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 549) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339659185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659185 none CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 29, 18, 12, 18, 12, 12, 2, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 40, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 550) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339659185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001339659185 none CCC(=O)NCC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 41, 24, 18, 10, 18, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 41, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659185 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659185 Building ZINC001339659562 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659562 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/551 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659562 none C[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 6, 15, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 15, 15, 24, 24, 37, 41, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 37, 37, 41, 41, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/552 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/552' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659562 none C[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 21, 21, 37, 41, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 37, 37, 41, 41, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659562 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562 Building ZINC001339659562 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659562 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 551) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659562 none C[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 6, 15, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 15, 15, 24, 24, 37, 41, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 37, 37, 41, 41, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 552) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659562 none C[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 21, 21, 37, 41, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 37, 37, 41, 41, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659562 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659562 Building ZINC001339659563 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659563 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/553 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659563 none C[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 22, 22, 38, 42, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 38, 38, 42, 42, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/554 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/554' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659563 none C[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 24, 24, 36, 41, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 36, 36, 41, 41, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659563 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563 Building ZINC001339659563 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659563 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 553) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659563 none C[C@@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 22, 22, 38, 42, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 38, 38, 42, 42, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 554) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659563 none C[C@@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 24, 24, 36, 41, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 36, 36, 41, 41, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659563 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659563 Building ZINC001339659564 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659564 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/555 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659564 none C[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 20, 20, 35, 39, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 39, 39, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/556 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/556' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659564 none C[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 5, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 16, 35, 39, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 35, 35, 39, 39, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659564 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564 Building ZINC001339659564 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659564 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 555) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659564 none C[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 20, 20, 35, 39, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 39, 39, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 556) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659564 none C[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 5, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 16, 35, 39, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 35, 35, 39, 39, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659564 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659564 Building ZINC001339659565 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659565 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/557 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659565 none C[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 20, 20, 37, 41, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 37, 37, 41, 41, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/558 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/558' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659565 none C[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 24, 24, 39, 42, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 39, 39, 42, 42, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659565 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565 Building ZINC001339659565 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339659565 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 557) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339659565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659565 none C[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 20, 20, 37, 41, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 37, 37, 41, 41, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 558) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1) `ZINC001339659565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339659565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339659565 none C[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CN1C(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 24, 24, 39, 42, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 39, 39, 42, 42, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339659565 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339659565 Building ZINC001339660721 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339660721 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/559 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339660721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339660721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660721 none Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 22, 43, 22, 22, 6, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22] 50 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, 46, 47, 48]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/560 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/560' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339660721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339660721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660721 none Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 18, 38, 18, 18, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 50, 50, 50, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18] 50 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, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339660721 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721 Building ZINC001339660721 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339660721 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 559) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339660721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339660721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660721 none Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 22, 43, 22, 22, 6, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22] 50 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, 46, 47, 48]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 560) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339660721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339660721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660721 none Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 18, 38, 18, 18, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 50, 50, 50, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18] 50 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, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339660721 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660721 Building ZINC001339660722 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339660722 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/561 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339660722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339660722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660722 none Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 40, 24, 40, 24, 24, 4, 24, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 50, 50, 50, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24] 50 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, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/562 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339660722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339660722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660722 none Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 24, 38, 24, 24, 4, 24, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 50, 50, 50, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24] 50 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, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339660722 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722 Building ZINC001339660722 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339660722 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 561) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339660722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339660722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660722 none Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 40, 24, 40, 24, 24, 4, 24, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 50, 50, 50, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24] 50 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, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 562) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339660722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339660722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660722 none Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 24, 38, 24, 24, 4, 24, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 50, 50, 50, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24] 50 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, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339660722 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660722 Building ZINC001339660723 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339660723 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/563 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339660723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339660723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660723 none Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 37, 20, 37, 20, 20, 5, 20, 3, 1, 3, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 20, 20, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20] 50 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, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/564 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/564' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339660723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339660723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660723 none Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 26, 39, 26, 26, 6, 26, 4, 1, 4, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 50, 50, 50, 26, 26, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26] 50 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, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339660723 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723 Building ZINC001339660723 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339660723 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 563) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339660723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339660723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660723 none Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 37, 20, 37, 20, 20, 5, 20, 3, 1, 3, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 20, 20, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20] 50 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, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 564) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339660723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339660723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660723 none Cc1nn[nH]c1C(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 26, 39, 26, 26, 6, 26, 4, 1, 4, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 50, 50, 50, 26, 26, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26] 50 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, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339660723 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660723 Building ZINC001339660724 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339660724 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/565 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339660724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339660724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660724 none Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 26, 39, 26, 26, 8, 26, 4, 1, 4, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 50, 50, 50, 26, 26, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26] 50 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, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/566 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339660724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339660724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660724 none Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 20, 36, 20, 20, 6, 20, 3, 1, 3, 1, 1, 1, 2, 2, 2, 20, 20, 20, 20, 20, 50, 50, 50, 20, 20, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339660724 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724 Building ZINC001339660724 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339660724 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 565) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339660724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339660724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660724 none Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 26, 39, 26, 26, 8, 26, 4, 1, 4, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 50, 50, 50, 26, 26, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26] 50 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, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 566) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339660724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339660724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339660724 none Cc1nn[nH]c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 20, 36, 20, 20, 6, 20, 3, 1, 3, 1, 1, 1, 2, 2, 2, 20, 20, 20, 20, 20, 50, 50, 50, 20, 20, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339660724 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339660724 Building ZINC001339663981 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339663981 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/567 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339663981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339663981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663981 none CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 22, 13, 22, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 42, 42, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/568 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339663981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339663981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663981 none CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 25, 15, 25, 15, 15, 4, 15, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 50, 40, 40, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339663981 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981 Building ZINC001339663981 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339663981 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 567) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339663981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339663981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663981 none CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 22, 13, 22, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 42, 42, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 568) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339663981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339663981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663981 none CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 25, 15, 25, 15, 15, 4, 15, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 50, 40, 40, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339663981 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663981 Building ZINC001339663982 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339663982 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/569 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339663982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339663982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663982 none CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 22, 13, 22, 13, 13, 6, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 42, 42, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/570 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339663982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339663982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663982 none CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 50, 21, 12, 21, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50, 50, 38, 38, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339663982 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982 Building ZINC001339663982 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339663982 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 569) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339663982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339663982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663982 none CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 22, 13, 22, 13, 13, 6, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 42, 42, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 570) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C) `ZINC001339663982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339663982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663982 none CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 50, 21, 12, 21, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50, 50, 38, 38, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339663982 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663982 Building ZINC001339663983 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339663983 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/571 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339663983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339663983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663983 none CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 23, 15, 23, 15, 15, 4, 15, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 50, 40, 40, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 183 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/572 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/572' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339663983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339663983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663983 none CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 22, 14, 22, 14, 14, 3, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 50, 43, 43, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339663983 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983 Building ZINC001339663983 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339663983 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 571) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339663983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339663983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663983 none CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 23, 15, 23, 15, 15, 4, 15, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50, 50, 50, 40, 40, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 183 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 572) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339663983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339663983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663983 none CNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 22, 14, 22, 14, 14, 3, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 50, 43, 43, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339663983 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663983 Building ZINC001339663984 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339663984 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/573 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339663984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339663984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663984 none CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 19, 11, 19, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50, 50, 50, 37, 37, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/574 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339663984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339663984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663984 none CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 20, 12, 20, 12, 12, 6, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50, 50, 41, 41, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339663984 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984 Building ZINC001339663984 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339663984 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 573) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339663984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339663984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663984 none CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 19, 11, 19, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50, 50, 50, 37, 37, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 574) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C) `ZINC001339663984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339663984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001339663984 none CNC(=O)CC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 20, 12, 20, 12, 12, 6, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50, 50, 41, 41, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339663984 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339663984 Building ZINC001339736610 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339736610 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/575 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1) `ZINC001339736610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339736610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736610 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 25, 25, 25, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 25, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/2379/xbv-8058097.48/working/building/ZINC001339736610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/576 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/576' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1) `ZINC001339736610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339736610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736610 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 22, 22, 22, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 22, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339736610 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610 Building ZINC001339736610 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339736610 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 575) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1) `ZINC001339736610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339736610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736610 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 25, 25, 25, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 25, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/2379/xbv-8058097.48/working/building/ZINC001339736610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 576) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1) `ZINC001339736610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339736610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736610 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 22, 22, 22, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 22, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339736610 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736610 Building ZINC001339736611 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339736611 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/577 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1) `ZINC001339736611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339736611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736611 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 18, 18, 18, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 18, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/578 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/578' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1) `ZINC001339736611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339736611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736611 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 8, 23, 23, 23, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 23, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339736611 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611 Building ZINC001339736611 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339736611 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 577) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1) `ZINC001339736611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339736611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736611 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 18, 18, 18, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 18, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 578) grep: /scratch/xiaobo/2379/xbv-8058097.48/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]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1) `ZINC001339736611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339736611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736611 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 8, 23, 23, 23, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 23, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339736611 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736611 Building ZINC001339736613 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339736613 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/579 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1) `ZINC001339736613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339736613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736613 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 21, 21, 21, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 21, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/580 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/580' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1) `ZINC001339736613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339736613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736613 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 2, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 20, 20, 20, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 20, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/2379/xbv-8058097.48/working/building/ZINC001339736613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339736613 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613 Building ZINC001339736613 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339736613 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 579) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1) `ZINC001339736613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339736613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736613 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 21, 21, 21, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 21, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 580) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1) `ZINC001339736613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339736613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736613 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 2, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 20, 20, 20, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 20, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/2379/xbv-8058097.48/working/building/ZINC001339736613 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339736613 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736613 Building ZINC001339736614 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339736614 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/581 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1) `ZINC001339736614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339736614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736614 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 10, 24, 24, 24, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 24, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/582 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/582' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1) `ZINC001339736614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339736614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736614 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 27, 27, 27, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 27, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339736614 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614 Building ZINC001339736614 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339736614 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 581) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1) `ZINC001339736614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339736614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736614 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 10, 24, 24, 24, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 24, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 582) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1) `ZINC001339736614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339736614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001339736614 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1CNC(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 27, 27, 27, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 27, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339736614 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339736614 Building ZINC001339760971 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339760971 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/583 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339760971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760971 none Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 40, 31, 40, 31, 31, 31, 31, 31, 31, 18, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/584 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/584' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339760971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760971 none Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 31, 41, 31, 31, 31, 31, 31, 31, 20, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339760971 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971 Building ZINC001339760971 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339760971 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 583) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339760971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760971 none Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 40, 31, 40, 31, 31, 31, 31, 31, 31, 18, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 584) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339760971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760971 none Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 31, 41, 31, 31, 31, 31, 31, 31, 20, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339760971 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760971 Building ZINC001339760972 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339760972 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/585 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339760972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760972 none Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 26, 45, 26, 26, 26, 26, 26, 26, 11, 26, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 26, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 26, 26] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/586 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339760972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760972 none Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 27, 43, 27, 27, 27, 27, 27, 27, 14, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339760972 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972 Building ZINC001339760972 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339760972 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 585) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339760972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760972 none Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 26, 45, 26, 26, 26, 26, 26, 26, 11, 26, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 26, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 26, 26] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 586) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339760972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760972 none Cc1nn[nH]c1C(=O)N1CC[C@H](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 27, 43, 27, 27, 27, 27, 27, 27, 14, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339760972 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760972 Building ZINC001339760973 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339760973 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/587 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339760973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760973 none Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 31, 42, 31, 31, 31, 31, 31, 31, 18, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/588 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339760973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760973 none Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 37, 25, 37, 25, 25, 25, 25, 25, 25, 14, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339760973 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973 Building ZINC001339760973 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339760973 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 587) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339760973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760973 none Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 31, 42, 31, 31, 31, 31, 31, 31, 18, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 588) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339760973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760973 none Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 37, 25, 37, 25, 25, 25, 25, 25, 25, 14, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339760973 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760973 Building ZINC001339760974 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339760974 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/589 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339760974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760974 none Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 30, 41, 30, 30, 30, 30, 30, 30, 18, 30, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 30, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/590 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339760974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760974 none Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 26, 41, 26, 26, 26, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339760974 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974 Building ZINC001339760974 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339760974 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 589) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339760974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760974 none Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 30, 41, 30, 30, 30, 30, 30, 30, 18, 30, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 30, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 590) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339760974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339760974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001339760974 none Cc1nn[nH]c1C(=O)N1CC[C@@H](C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 26, 41, 26, 26, 26, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339760974 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339760974 Building ZINC001339782861 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339782861 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/591 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1) `ZINC001339782861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339782861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001339782861 none C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 36, 10, 3, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 27, 27, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/592 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1) `ZINC001339782861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339782861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001339782861 none C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 28, 41, 13, 3, 13, 13, 3, 1, 3, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 28, 28, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339782861 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861 Building ZINC001339782861 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339782861 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 591) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1) `ZINC001339782861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339782861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001339782861 none C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 36, 10, 3, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 27, 27, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 592) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1) `ZINC001339782861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339782861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001339782861 none C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 28, 41, 13, 3, 13, 13, 3, 1, 3, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 28, 28, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339782861 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782861 Building ZINC001339782864 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339782864 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/593 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)c1cc[n+]([O-])cc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339782864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339782864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339782864 none C[C@H](C[C@H](C)NC(=O)c1cc[n+]([O-])cc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [13, 3, 13, 13, 28, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 28, 28, 41, 41, 41, 50, 50, 50, 50, 50, 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: 211 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/594 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)c1cc[n+]([O-])cc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339782864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339782864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339782864 none C[C@H](C[C@H](C)NC(=O)c1cc[n+]([O-])cc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [11, 3, 11, 11, 28, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 28, 28, 37, 37, 37, 50, 50, 50, 50, 50, 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: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339782864 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864 Building ZINC001339782864 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339782864 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 593) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)c1cc[n+]([O-])cc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339782864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339782864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339782864 none C[C@H](C[C@H](C)NC(=O)c1cc[n+]([O-])cc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [13, 3, 13, 13, 28, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 28, 28, 41, 41, 41, 50, 50, 50, 50, 50, 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: 211 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 594) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)c1cc[n+]([O-])cc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339782864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339782864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339782864 none C[C@H](C[C@H](C)NC(=O)c1cc[n+]([O-])cc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [11, 3, 11, 11, 28, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 28, 28, 37, 37, 37, 50, 50, 50, 50, 50, 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: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339782864 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782864 Building ZINC001339782867 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339782867 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/595 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1) `ZINC001339782867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339782867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001339782867 none C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 35, 10, 2, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 21, 21, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/596 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/596' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1) `ZINC001339782867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339782867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001339782867 none C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 22, 39, 9, 2, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 49, 50, 49, 50, 50, 50, 50, 50, 50, 39, 39, 39, 24, 24, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 223 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339782867 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867 Building ZINC001339782867 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339782867 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 595) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1) `ZINC001339782867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339782867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001339782867 none C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 35, 10, 2, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 21, 21, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 596) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1) `ZINC001339782867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339782867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001339782867 none C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 22, 39, 9, 2, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 49, 50, 49, 50, 50, 50, 50, 50, 50, 39, 39, 39, 24, 24, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 223 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339782867 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782867 Building ZINC001339782869 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339782869 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/597 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1) `ZINC001339782869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339782869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001339782869 none C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 22, 39, 9, 2, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 49, 50, 49, 50, 50, 50, 50, 50, 50, 39, 39, 39, 24, 24, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 223 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/598 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/598' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1) `ZINC001339782869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339782869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001339782869 none C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 36, 10, 2, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 21, 21, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339782869 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869 Building ZINC001339782869 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339782869 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 597) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1) `ZINC001339782869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339782869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001339782869 none C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 22, 39, 9, 2, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 49, 50, 49, 50, 50, 50, 50, 50, 50, 39, 39, 39, 24, 24, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 223 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 598) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1) `ZINC001339782869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339782869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001339782869 none C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc[n+]([O-])cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 36, 10, 2, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 21, 21, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339782869 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339782869 Building ZINC001339803299 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339803299 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/599 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339803299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339803299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339803299 none C[C@H](C[C@@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 19, 19, 19, 25, 25, 25, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 19, 19, 19, 25, 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: 196 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/600 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/600' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339803299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339803299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339803299 none C[C@H](C[C@@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 20, 20, 20, 27, 27, 27, 50, 50, 50, 50, 50, 50, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 20, 20, 20, 27, 50, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339803299 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299 Building ZINC001339803299 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339803299 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 599) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339803299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339803299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339803299 none C[C@H](C[C@@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 19, 19, 19, 25, 25, 25, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 19, 19, 19, 25, 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: 196 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 600) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339803299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339803299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339803299 none C[C@H](C[C@@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 20, 20, 20, 27, 27, 27, 50, 50, 50, 50, 50, 50, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 20, 20, 20, 27, 50, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339803299 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803299 Building ZINC001339803301 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339803301 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/601 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339803301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339803301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339803301 none C[C@@H](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 24, 24, 24, 50, 50, 50, 50, 50, 50, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 19, 19, 19, 24, 50, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/602 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/602' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339803301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339803301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339803301 none C[C@@H](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 28, 28, 28, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 20, 20, 20, 28, 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: 189 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339803301 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301 Building ZINC001339803301 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339803301 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 601) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339803301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339803301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339803301 none C[C@@H](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 24, 24, 24, 50, 50, 50, 50, 50, 50, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 19, 19, 19, 24, 50, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 602) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339803301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339803301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339803301 none C[C@@H](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 28, 28, 28, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 20, 20, 20, 28, 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: 189 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339803301 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803301 Building ZINC001339803303 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339803303 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/603 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C1(NC(N)=O)CC1) `ZINC001339803303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339803303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339803303 none C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C1(NC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 19, 9, 3, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 19, 26, 26, 26, 49, 50, 50, 50, 49, 49, 19, 19, 19, 13, 13, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 49, 49, 49, 49] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/604 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C1(NC(N)=O)CC1) `ZINC001339803303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339803303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339803303 none C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C1(NC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 14, 17, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 23, 23, 49, 50, 50, 50, 49, 49, 17, 17, 17, 14, 14, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 49, 49, 49, 49] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339803303 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303 Building ZINC001339803303 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339803303 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 603) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C1(NC(N)=O)CC1) `ZINC001339803303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339803303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339803303 none C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C1(NC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 19, 9, 3, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 19, 26, 26, 26, 49, 50, 50, 50, 49, 49, 19, 19, 19, 13, 13, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 49, 49, 49, 49] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 604) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C1(NC(N)=O)CC1) `ZINC001339803303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339803303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339803303 none C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C1(NC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 14, 17, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 23, 23, 49, 50, 50, 50, 49, 49, 17, 17, 17, 14, 14, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 49, 49, 49, 49] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339803303 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803303 Building ZINC001339803305 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339803305 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/605 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339803305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339803305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339803305 none C[C@H](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 20, 20, 20, 24, 24, 24, 49, 50, 50, 50, 49, 49, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 15, 15, 20, 20, 20, 24, 50, 50, 50, 49, 49, 49, 49, 3, 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: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/606 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339803305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339803305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339803305 none C[C@H](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 20, 20, 20, 28, 28, 28, 49, 50, 50, 50, 49, 49, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 20, 20, 20, 28, 50, 50, 50, 49, 49, 49, 49, 3, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339803305 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305 Building ZINC001339803305 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339803305 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 605) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339803305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339803305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339803305 none C[C@H](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 20, 20, 20, 24, 24, 24, 49, 50, 50, 50, 49, 49, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 15, 15, 20, 20, 20, 24, 50, 50, 50, 49, 49, 49, 49, 3, 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: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 606) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339803305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339803305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339803305 none C[C@H](C[C@H](C)NC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 20, 20, 20, 28, 28, 28, 49, 50, 50, 50, 49, 49, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 20, 20, 20, 28, 50, 50, 50, 49, 49, 49, 49, 3, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339803305 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339803305 Building ZINC001339806592 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339806592 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/607 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N) `ZINC001339806592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339806592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339806592 none C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 29, 29, 29, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/608 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/608' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N) `ZINC001339806592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339806592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339806592 none C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 22, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 32, 32, 32, 50, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339806592 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592 Building ZINC001339806592 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339806592 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 607) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N) `ZINC001339806592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339806592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339806592 none C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 29, 29, 29, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 608) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N) `ZINC001339806592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339806592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339806592 none C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 22, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 32, 32, 32, 50, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339806592 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806592 Building ZINC001339806597 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339806597 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/609 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N) `ZINC001339806597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339806597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339806597 none C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 21, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 32, 32, 32, 50, 50, 50, 50, 50, 50, 21, 21, 21, 14, 14, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/610 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/610' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N) `ZINC001339806597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339806597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339806597 none C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 28, 28, 28, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339806597 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597 Building ZINC001339806597 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339806597 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 609) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N) `ZINC001339806597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339806597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339806597 none C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 21, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 32, 32, 32, 50, 50, 50, 50, 50, 50, 21, 21, 21, 14, 14, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 610) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N) `ZINC001339806597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339806597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339806597 none C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 28, 28, 28, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339806597 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806597 Building ZINC001339806601 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339806601 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/611 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)c1cnn(C)c1N)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339806601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339806601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339806601 none C[C@H](C[C@H](C)NC(=O)c1cnn(C)c1N)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 17, 25, 25, 25, 33, 33, 33, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 25, 25, 25, 33, 50, 50, 50, 50, 50, 50, 2, 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: 164 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/612 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)c1cnn(C)c1N)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339806601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339806601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339806601 none C[C@H](C[C@H](C)NC(=O)c1cnn(C)c1N)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens 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, 19, 24, 24, 24, 31, 31, 31, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 24, 24, 24, 31, 50, 50, 50, 50, 50, 50, 2, 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: 172 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339806601 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601 Building ZINC001339806601 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339806601 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 611) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)c1cnn(C)c1N)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339806601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339806601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339806601 none C[C@H](C[C@H](C)NC(=O)c1cnn(C)c1N)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 17, 25, 25, 25, 33, 33, 33, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 25, 25, 25, 33, 50, 50, 50, 50, 50, 50, 2, 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: 164 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 612) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)c1cnn(C)c1N)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339806601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339806601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339806601 none C[C@H](C[C@H](C)NC(=O)c1cnn(C)c1N)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens 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, 19, 24, 24, 24, 31, 31, 31, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 24, 24, 24, 31, 50, 50, 50, 50, 50, 50, 2, 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: 172 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339806601 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806601 Building ZINC001339806607 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339806607 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/613 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N) `ZINC001339806607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339806607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339806607 none C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 24, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 30, 50, 50, 50, 50, 50, 50, 24, 24, 24, 19, 19, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/614 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/614' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N) `ZINC001339806607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339806607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339806607 none C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 16, 23, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 30, 30, 30, 50, 50, 50, 50, 50, 50, 23, 23, 23, 16, 16, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339806607 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607 Building ZINC001339806607 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339806607 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 613) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N) `ZINC001339806607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339806607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339806607 none C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 24, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 30, 50, 50, 50, 50, 50, 50, 24, 24, 24, 19, 19, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 614) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N) `ZINC001339806607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339806607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339806607 none C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 16, 23, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 30, 30, 30, 50, 50, 50, 50, 50, 50, 23, 23, 23, 16, 16, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339806607 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339806607 Building ZINC001339812669 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339812669 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/615 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1) `ZINC001339812669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339812669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812669 none C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 29, 36, 50, 50, 50, 50, 50, 13, 13, 13, 10, 10, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 29, 29, 36, 36, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/616 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/616' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1) `ZINC001339812669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339812669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812669 none C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 16, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 16, 20, 20, 20, 42, 45, 50, 50, 50, 50, 50, 16, 16, 16, 11, 11, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 42, 42, 45, 45, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 212 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339812669 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669 Building ZINC001339812669 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339812669 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 615) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1) `ZINC001339812669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339812669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812669 none C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 29, 36, 50, 50, 50, 50, 50, 13, 13, 13, 10, 10, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 29, 29, 36, 36, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 616) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1) `ZINC001339812669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339812669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812669 none C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 16, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 16, 20, 20, 20, 42, 45, 50, 50, 50, 50, 50, 16, 16, 16, 11, 11, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 42, 42, 45, 45, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 212 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339812669 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812669 Building ZINC001339812670 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339812670 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/617 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1) `ZINC001339812670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339812670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812670 none C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 19, 19, 19, 31, 38, 50, 50, 50, 50, 50, 14, 14, 14, 9, 9, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 31, 31, 38, 38, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/618 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/618' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1) `ZINC001339812670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339812670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812670 none C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 16, 16, 16, 37, 44, 50, 50, 50, 50, 50, 12, 12, 12, 8, 8, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 37, 37, 44, 44, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339812670 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670 Building ZINC001339812670 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339812670 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 617) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1) `ZINC001339812670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339812670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812670 none C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 19, 19, 19, 31, 38, 50, 50, 50, 50, 50, 14, 14, 14, 9, 9, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 31, 31, 38, 38, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 618) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1) `ZINC001339812670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339812670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812670 none C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 16, 16, 16, 37, 44, 50, 50, 50, 50, 50, 12, 12, 12, 8, 8, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 37, 37, 44, 44, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339812670 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812670 Building ZINC001339812671 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339812671 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/619 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1) `ZINC001339812671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339812671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812671 none C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 15, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 19, 19, 19, 39, 44, 50, 50, 50, 50, 50, 15, 15, 15, 12, 12, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 39, 39, 44, 44, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 202 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/620 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/620' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1) `ZINC001339812671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339812671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812671 none C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 16, 16, 16, 30, 37, 50, 50, 50, 50, 50, 14, 14, 14, 11, 11, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 30, 30, 37, 37, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 213 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339812671 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671 Building ZINC001339812671 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339812671 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 619) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1) `ZINC001339812671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339812671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812671 none C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 15, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 19, 19, 19, 39, 44, 50, 50, 50, 50, 50, 15, 15, 15, 12, 12, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 39, 39, 44, 44, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 202 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 620) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1) `ZINC001339812671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339812671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812671 none C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 16, 16, 16, 30, 37, 50, 50, 50, 50, 50, 14, 14, 14, 11, 11, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 30, 30, 37, 37, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 213 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339812671 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812671 Building ZINC001339812672 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339812672 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/621 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)CCc1cnn[nH]1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339812672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339812672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812672 none C[C@H](C[C@H](C)NC(=O)CCc1cnn[nH]1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 12, 12, 12, 17, 17, 17, 37, 45, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 12, 12, 12, 17, 37, 37, 45, 45, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 209 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/622 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)CCc1cnn[nH]1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339812672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339812672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812672 none C[C@H](C[C@H](C)NC(=O)CCc1cnn[nH]1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 14, 14, 14, 18, 18, 18, 32, 39, 50, 50, 50, 50, 50, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 9, 14, 14, 14, 18, 32, 32, 39, 39, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339812672 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672 Building ZINC001339812672 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339812672 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 621) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H](C[C@H](C)NC(=O)CCc1cnn[nH]1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339812672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339812672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812672 none C[C@H](C[C@H](C)NC(=O)CCc1cnn[nH]1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 12, 12, 12, 17, 17, 17, 37, 45, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 12, 12, 12, 17, 37, 37, 45, 45, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 209 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 622) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H](C[C@H](C)NC(=O)CCc1cnn[nH]1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339812672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339812672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001339812672 none C[C@H](C[C@H](C)NC(=O)CCc1cnn[nH]1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 14, 14, 14, 18, 18, 18, 32, 39, 50, 50, 50, 50, 50, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 9, 14, 14, 14, 18, 32, 32, 39, 39, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339812672 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339812672 Building ZINC001339813422 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813422 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/623 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C) `ZINC001339813422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339813422 none C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 15, 28, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 40, 40, 40, 50, 50, 50, 50, 50, 50, 28, 28, 28, 15, 15, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 50, 150, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/624 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C) `ZINC001339813422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339813422 none C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 26, 9, 2, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 39, 50, 50, 50, 50, 50, 50, 26, 26, 26, 17, 17, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 150, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813422 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422 Building ZINC001339813422 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813422 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 623) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C) `ZINC001339813422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339813422 none C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 15, 28, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 40, 40, 40, 50, 50, 50, 50, 50, 50, 28, 28, 28, 15, 15, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 50, 150, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 624) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C) `ZINC001339813422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339813422 none C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 26, 9, 2, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 39, 50, 50, 50, 50, 50, 50, 26, 26, 26, 17, 17, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 150, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813422 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813422 Building ZINC001339813424 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813424 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/625 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C) `ZINC001339813424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339813424 none C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 18, 28, 9, 2, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 44, 44, 44, 50, 50, 50, 50, 50, 50, 28, 28, 28, 18, 18, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 50, 150, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 347 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/626 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/626' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C) `ZINC001339813424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339813424 none C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 18, 31, 9, 2, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 44, 44, 44, 50, 50, 50, 50, 50, 50, 31, 31, 31, 18, 18, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 50, 150, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 345 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813424 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424 Building ZINC001339813424 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813424 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 625) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C) `ZINC001339813424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339813424 none C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 18, 28, 9, 2, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 44, 44, 44, 50, 50, 50, 50, 50, 50, 28, 28, 28, 18, 18, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 50, 150, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 347 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 626) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C) `ZINC001339813424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339813424 none C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 18, 31, 9, 2, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 44, 44, 44, 50, 50, 50, 50, 50, 50, 31, 31, 31, 18, 18, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 50, 150, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 345 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813424 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813424 Building ZINC001339813428 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813428 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/627 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)c1cnc(O)n1C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339813428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339813428 none C[C@H](C[C@H](C)NC(=O)c1cnc(O)n1C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 20, 30, 30, 30, 42, 42, 42, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 20, 20, 30, 30, 30, 42, 50, 150, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 336 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/628 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)c1cnc(O)n1C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339813428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339813428 none C[C@H](C[C@H](C)NC(=O)c1cnc(O)n1C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 26, 26, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 26, 26, 26, 36, 50, 150, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 333 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813428 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428 Building ZINC001339813428 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813428 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 627) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)c1cnc(O)n1C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339813428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339813428 none C[C@H](C[C@H](C)NC(=O)c1cnc(O)n1C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 20, 30, 30, 30, 42, 42, 42, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 20, 20, 30, 30, 30, 42, 50, 150, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 336 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 628) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)c1cnc(O)n1C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339813428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339813428 none C[C@H](C[C@H](C)NC(=O)c1cnc(O)n1C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 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, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 26, 26, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 26, 26, 26, 36, 50, 150, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 333 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813428 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813428 Building ZINC001339813430 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813430 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/629 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C) `ZINC001339813430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339813430 none C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 39, 39, 39, 50, 50, 50, 50, 50, 50, 28, 28, 28, 19, 19, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 150, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 339 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/630 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/630' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C) `ZINC001339813430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339813430 none C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 32, 10, 2, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 42, 42, 42, 50, 50, 50, 50, 50, 50, 32, 32, 32, 21, 21, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 50, 150, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 348 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813430 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430 Building ZINC001339813430 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813430 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 629) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C) `ZINC001339813430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339813430 none C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 39, 39, 39, 50, 50, 50, 50, 50, 50, 28, 28, 28, 19, 19, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 150, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 339 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 630) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C) `ZINC001339813430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001339813430 none C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 32, 10, 2, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 42, 42, 42, 50, 50, 50, 50, 50, 50, 32, 32, 32, 21, 21, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 50, 150, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 348 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813430 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813430 Building ZINC001339813672 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813672 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/631 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1) `ZINC001339813672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001339813672 none C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 23, 23, 23, 43, 50, 50, 7, 7, 7, 4, 4, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/632 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1) `ZINC001339813672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001339813672 none C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 18, 18, 18, 23, 23, 23, 44, 50, 50, 13, 13, 13, 8, 8, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 23, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813672 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672 Building ZINC001339813672 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813672 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 631) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1) `ZINC001339813672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001339813672 none C[C@H](C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 23, 23, 23, 43, 50, 50, 7, 7, 7, 4, 4, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 632) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1) `ZINC001339813672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001339813672 none C[C@H](C[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 18, 18, 18, 23, 23, 23, 44, 50, 50, 13, 13, 13, 8, 8, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 23, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813672 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813672 Building ZINC001339813676 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813676 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/633 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)C(=O)NCC1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339813676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339813676 none C[C@H](C[C@H](C)NC(=O)C(=O)NCC1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [6, 2, 6, 6, 10, 13, 13, 13, 19, 19, 19, 28, 28, 28, 44, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 13, 13, 13, 19, 28, 44, 44, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 216 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/634 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/634' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)C(=O)NCC1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339813676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339813676 none C[C@H](C[C@H](C)NC(=O)C(=O)NCC1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [6, 2, 6, 6, 8, 10, 10, 10, 17, 17, 17, 29, 28, 28, 43, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 10, 10, 10, 17, 29, 43, 43, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 212 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813676 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676 Building ZINC001339813676 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813676 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 633) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)C(=O)NCC1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001339813676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339813676 none C[C@H](C[C@H](C)NC(=O)C(=O)NCC1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [6, 2, 6, 6, 10, 13, 13, 13, 19, 19, 19, 28, 28, 28, 44, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 13, 13, 13, 19, 28, 44, 44, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 216 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 634) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)C(=O)NCC1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001339813676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001339813676 none C[C@H](C[C@H](C)NC(=O)C(=O)NCC1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [6, 2, 6, 6, 8, 10, 10, 10, 17, 17, 17, 29, 28, 28, 43, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 10, 10, 10, 17, 29, 43, 43, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 212 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813676 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813676 Building ZINC001339813679 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813679 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/635 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1) `ZINC001339813679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001339813679 none C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 26, 26, 26, 40, 50, 50, 10, 10, 10, 6, 6, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 26, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/636 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1) `ZINC001339813679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001339813679 none C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 21, 21, 21, 24, 24, 24, 41, 50, 50, 14, 14, 14, 9, 9, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 24, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813679 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679 Building ZINC001339813679 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813679 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 635) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1) `ZINC001339813679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001339813679 none C[C@@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 26, 26, 26, 40, 50, 50, 10, 10, 10, 6, 6, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 26, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 636) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1) `ZINC001339813679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001339813679 none C[C@@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 21, 21, 21, 24, 24, 24, 41, 50, 50, 14, 14, 14, 9, 9, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 24, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813679 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813679 Building ZINC001339813683 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813683 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/637 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1) `ZINC001339813683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001339813683 none C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 17, 17, 17, 30, 29, 29, 44, 50, 50, 11, 11, 11, 7, 7, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 30, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/638 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/638' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1) `ZINC001339813683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001339813683 none C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 15, 25, 25, 25, 38, 50, 50, 11, 11, 11, 9, 9, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 25, 38, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813683 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683 Building ZINC001339813683 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339813683 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 637) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1) `ZINC001339813683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339813683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001339813683 none C[C@H](C[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 17, 17, 17, 30, 29, 29, 44, 50, 50, 11, 11, 11, 7, 7, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 30, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 638) grep: /scratch/xiaobo/2379/xbv-8058097.48/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](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1) `ZINC001339813683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339813683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001339813683 none C[C@H](C[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 15, 25, 25, 25, 38, 50, 50, 11, 11, 11, 9, 9, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 25, 38, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339813683 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339813683 Building ZINC001339883941 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339883941 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/639 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(C(=O)C(=O)NCC1CC1)C2) `ZINC001339883941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339883941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339883941 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(C(=O)C(=O)NCC1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 6, 7, 7, 7, 7, 7, 7, 7, 11, 11, 25, 25, 25, 39, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 25, 39, 39, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/640 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/640' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(C(=O)C(=O)NCC1CC1)C2) `ZINC001339883941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339883941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339883941 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(C(=O)C(=O)NCC1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 8, 11, 11, 11, 11, 11, 11, 11, 15, 15, 26, 26, 26, 41, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 26, 41, 41, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339883941 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941 Building ZINC001339883941 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339883941 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 639) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(C(=O)C(=O)NCC1CC1)C2) `ZINC001339883941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339883941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339883941 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(C(=O)C(=O)NCC1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 6, 7, 7, 7, 7, 7, 7, 7, 11, 11, 25, 25, 25, 39, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 25, 39, 39, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 640) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(C(=O)C(=O)NCC1CC1)C2) `ZINC001339883941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339883941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001339883941 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(C(=O)C(=O)NCC1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 8, 11, 11, 11, 11, 11, 11, 11, 15, 15, 26, 26, 26, 41, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 26, 41, 41, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339883941 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339883941 Building ZINC001339884873 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339884873 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/641 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001339884873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339884873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339884873 none COC(=O)NCC(=O)N1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 26, 16, 12, 16, 12, 12, 12, 12, 12, 4, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 36, 26, 26, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/642 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/642' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001339884873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339884873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339884873 none COC(=O)NCC(=O)N1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 50, 24, 11, 7, 11, 7, 7, 7, 7, 7, 2, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 35, 24, 24, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339884873 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873 Building ZINC001339884873 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339884873 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 641) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)NCC(=O)N1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001339884873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339884873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339884873 none COC(=O)NCC(=O)N1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 26, 16, 12, 16, 12, 12, 12, 12, 12, 4, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 36, 26, 26, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 642) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)NCC(=O)N1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001339884873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339884873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339884873 none COC(=O)NCC(=O)N1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 50, 24, 11, 7, 11, 7, 7, 7, 7, 7, 2, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 35, 24, 24, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339884873 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339884873 Building ZINC001339977015 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339977015 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/643 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2cc[nH]c2)CCCO1) `ZINC001339977015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339977015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339977015 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2cc[nH]c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 6, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 28, 28, 28, 28, 33, 33, 50, 50, 50, 50, 50, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 50, 50, 50, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/644 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/644' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2cc[nH]c2)CCCO1) `ZINC001339977015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339977015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339977015 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2cc[nH]c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 6, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 37, 37, 37, 37, 38, 38, 50, 50, 50, 50, 50, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 37, 37, 50, 50, 50, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339977015 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015 Building ZINC001339977015 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339977015 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 643) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2cc[nH]c2)CCCO1) `ZINC001339977015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339977015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339977015 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2cc[nH]c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 6, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 28, 28, 28, 28, 33, 33, 50, 50, 50, 50, 50, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 50, 50, 50, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 644) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2cc[nH]c2)CCCO1) `ZINC001339977015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339977015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339977015 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2cc[nH]c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 6, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 37, 37, 37, 37, 38, 38, 50, 50, 50, 50, 50, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 37, 37, 50, 50, 50, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339977015 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977015 Building ZINC001339977018 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339977018 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/645 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2cc[nH]c2)CCCO1) `ZINC001339977018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339977018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339977018 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2cc[nH]c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 6, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 38, 38, 50, 50, 50, 50, 50, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 32, 32, 50, 50, 50, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/646 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/646' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2cc[nH]c2)CCCO1) `ZINC001339977018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339977018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339977018 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2cc[nH]c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 6, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 25, 25, 25, 25, 29, 29, 50, 50, 50, 50, 50, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 25, 25, 50, 50, 50, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339977018 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018 Building ZINC001339977018 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339977018 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 645) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2cc[nH]c2)CCCO1) `ZINC001339977018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339977018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339977018 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2cc[nH]c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 6, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 38, 38, 50, 50, 50, 50, 50, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 32, 32, 50, 50, 50, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 646) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2cc[nH]c2)CCCO1) `ZINC001339977018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339977018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339977018 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2cc[nH]c2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 6, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 25, 25, 25, 25, 29, 29, 50, 50, 50, 50, 50, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 25, 25, 50, 50, 50, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339977018 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339977018 Building ZINC001339979165 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339979165 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/647 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/647' -> `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]1CN(C(=O)c2ccnnc2)CCCO1) `ZINC001339979165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339979165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339979165 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2ccnnc2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 40, 40, 40, 40, 43, 43, 50, 50, 50, 50, 50, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 40, 40, 50, 50, 50, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/648 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/648' -> `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]1CN(C(=O)c2ccnnc2)CCCO1) `ZINC001339979165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339979165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339979165 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2ccnnc2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 37, 37, 37, 37, 41, 41, 50, 50, 50, 50, 50, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 37, 37, 50, 50, 50, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339979165 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165 Building ZINC001339979165 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339979165 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 647) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2ccnnc2)CCCO1) `ZINC001339979165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339979165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339979165 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2ccnnc2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 40, 40, 40, 40, 43, 43, 50, 50, 50, 50, 50, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 40, 40, 50, 50, 50, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 648) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2ccnnc2)CCCO1) `ZINC001339979165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339979165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339979165 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(C(=O)c2ccnnc2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 37, 37, 37, 37, 41, 41, 50, 50, 50, 50, 50, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 37, 37, 50, 50, 50, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339979165 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979165 Building ZINC001339979166 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339979166 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/649 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2ccnnc2)CCCO1) `ZINC001339979166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339979166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339979166 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2ccnnc2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 36, 36, 36, 36, 40, 40, 50, 50, 50, 50, 50, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 36, 36, 50, 50, 50, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/650 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/650' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2ccnnc2)CCCO1) `ZINC001339979166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339979166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339979166 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2ccnnc2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 43, 43, 43, 43, 44, 44, 50, 50, 50, 50, 50, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 43, 43, 50, 50, 50, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339979166 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166 Building ZINC001339979166 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339979166 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 649) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2ccnnc2)CCCO1) `ZINC001339979166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339979166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339979166 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2ccnnc2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 36, 36, 36, 36, 40, 40, 50, 50, 50, 50, 50, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 36, 36, 50, 50, 50, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 650) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2ccnnc2)CCCO1) `ZINC001339979166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339979166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339979166 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(C(=O)c2ccnnc2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 43, 43, 43, 43, 44, 44, 50, 50, 50, 50, 50, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 43, 43, 50, 50, 50, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339979166 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339979166 Building ZINC001339980982 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339980982 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/651 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CCCO[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339980982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339980982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339980982 none COCCCC(=O)N1CCCO[C@H](CNC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 38, 26, 26, 26, 26, 26, 26, 26, 26, 16, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 39, 39, 38, 38, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/652 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CCCO[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339980982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339980982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339980982 none COCCCC(=O)N1CCCO[C@H](CNC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 22, 21, 22, 21, 21, 21, 21, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 37, 37, 36, 36, 21, 21, 21, 21, 21, 21, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339980982 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982 Building ZINC001339980982 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339980982 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 651) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCCC(=O)N1CCCO[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339980982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339980982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339980982 none COCCCC(=O)N1CCCO[C@H](CNC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 38, 26, 26, 26, 26, 26, 26, 26, 26, 16, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 39, 39, 38, 38, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 652) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCCC(=O)N1CCCO[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339980982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339980982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339980982 none COCCCC(=O)N1CCCO[C@H](CNC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 22, 21, 22, 21, 21, 21, 21, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 37, 37, 36, 36, 21, 21, 21, 21, 21, 21, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339980982 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980982 Building ZINC001339980983 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339980983 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/653 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CCCO[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339980983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339980983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339980983 none COCCCC(=O)N1CCCO[C@@H](CNC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 20, 19, 20, 19, 19, 19, 19, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 49, 50, 37, 37, 35, 35, 19, 19, 19, 19, 19, 19, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/654 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/654' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CCCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339980983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339980983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339980983 none COCCCC(=O)N1CCCO[C@@H](CNC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 24, 24, 24, 24, 24, 24, 24, 24, 15, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 48, 50, 39, 39, 37, 37, 24, 24, 24, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339980983 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983 Building ZINC001339980983 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339980983 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 653) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCCC(=O)N1CCCO[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339980983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339980983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339980983 none COCCCC(=O)N1CCCO[C@@H](CNC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 20, 19, 20, 19, 19, 19, 19, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 49, 50, 37, 37, 35, 35, 19, 19, 19, 19, 19, 19, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 654) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCCC(=O)N1CCCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001339980983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339980983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001339980983 none COCCCC(=O)N1CCCO[C@@H](CNC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 24, 24, 24, 24, 24, 24, 24, 24, 15, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 48, 50, 39, 39, 37, 37, 24, 24, 24, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339980983 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339980983 Building ZINC001339986072 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339986072 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/655 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001339986072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339986072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339986072 none CC(C)[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 50, 35, 43, 43, 35, 35, 15, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 129, 35, 15, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/656 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001339986072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339986072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339986072 none CC(C)[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 50, 33, 43, 43, 33, 33, 14, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 129, 33, 14, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339986072 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072 Building ZINC001339986072 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339986072 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 655) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001339986072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339986072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339986072 none CC(C)[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 50, 35, 43, 43, 35, 35, 15, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 129, 35, 15, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 656) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001339986072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339986072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339986072 none CC(C)[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 50, 33, 43, 43, 33, 33, 14, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 129, 33, 14, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339986072 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986072 Building ZINC001339986074 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339986074 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/657 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001339986074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339986074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339986074 none CC(C)[C@@H](O)C(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 50, 39, 43, 43, 39, 39, 19, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 129, 39, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/658 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001339986074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339986074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339986074 none CC(C)[C@@H](O)C(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 50, 36, 41, 41, 36, 36, 19, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 123, 36, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339986074 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074 Building ZINC001339986074 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001339986074 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 657) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001339986074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339986074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339986074 none CC(C)[C@@H](O)C(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 50, 39, 43, 43, 39, 39, 19, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 129, 39, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 658) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001339986074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339986074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001339986074 none CC(C)[C@@H](O)C(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 50, 36, 41, 41, 36, 36, 19, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 123, 36, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001339986074 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001339986074 Building ZINC001340053058 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340053058 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/659 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCc1nc[nH]n1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340053058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340053058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340053058 none CCN(C(=O)CCc1nc[nH]n1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', '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, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 10, 15, 16, 16, 19, 19, 38, 38, 38, 38, 38, 7, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 19, 19, 19, 19, 38, 10, 10, 10, 7, 7, 2, 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: 143 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/660 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/660' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCc1nc[nH]n1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340053058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340053058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340053058 none CCN(C(=O)CCc1nc[nH]n1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', '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, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 11, 15, 15, 15, 15, 15, 44, 44, 44, 44, 44, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 15, 15, 15, 15, 44, 11, 11, 11, 8, 8, 2, 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: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340053058 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058 Building ZINC001340053058 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340053058 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 659) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)CCc1nc[nH]n1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340053058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340053058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340053058 none CCN(C(=O)CCc1nc[nH]n1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', '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, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 10, 15, 16, 16, 19, 19, 38, 38, 38, 38, 38, 7, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 19, 19, 19, 19, 38, 10, 10, 10, 7, 7, 2, 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: 143 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 660) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)CCc1nc[nH]n1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340053058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340053058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340053058 none CCN(C(=O)CCc1nc[nH]n1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', '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, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 11, 15, 15, 15, 15, 15, 44, 44, 44, 44, 44, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 15, 15, 15, 15, 44, 11, 11, 11, 8, 8, 2, 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: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340053058 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053058 Building ZINC001340053350 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340053350 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/661 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1OCCO[C@H]1C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340053350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340053350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001340053350 none CCN(C(=O)[C@H]1OCCO[C@H]1C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 35, 24, 35, 41, 44, 45, 45, 45, 45, 45, 45, 45, 45, 11, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 45, 45, 45, 45, 45, 45, 45, 24, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/662 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/662' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1OCCO[C@H]1C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340053350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340053350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001340053350 none CCN(C(=O)[C@H]1OCCO[C@H]1C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 33, 22, 33, 39, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 43, 43, 43, 43, 43, 43, 43, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 205 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340053350 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350 Building ZINC001340053350 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340053350 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 661) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@H]1OCCO[C@H]1C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340053350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340053350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001340053350 none CCN(C(=O)[C@H]1OCCO[C@H]1C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 35, 24, 35, 41, 44, 45, 45, 45, 45, 45, 45, 45, 45, 11, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 45, 45, 45, 45, 45, 45, 45, 24, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 662) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@H]1OCCO[C@H]1C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340053350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340053350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001340053350 none CCN(C(=O)[C@H]1OCCO[C@H]1C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 33, 22, 33, 39, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 43, 43, 43, 43, 43, 43, 43, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 205 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340053350 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053350 Building ZINC001340053412 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340053412 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/663 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)Cc1ccn(C)n1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340053412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340053412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001340053412 none CCN(C(=O)Cc1ccn(C)n1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 23, 17, 23, 26, 26, 42, 47, 47, 47, 47, 47, 9, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 42, 42, 47, 47, 47, 47, 47, 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: 242 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/664 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/664' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)Cc1ccn(C)n1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340053412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340053412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001340053412 none CCN(C(=O)Cc1ccn(C)n1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 17, 24, 28, 28, 43, 48, 48, 48, 48, 48, 10, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 43, 43, 48, 48, 48, 48, 48, 17, 17, 17, 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: 226 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340053412 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412 Building ZINC001340053412 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340053412 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 663) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)Cc1ccn(C)n1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340053412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340053412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001340053412 none CCN(C(=O)Cc1ccn(C)n1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 23, 17, 23, 26, 26, 42, 47, 47, 47, 47, 47, 9, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 42, 42, 47, 47, 47, 47, 47, 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: 242 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 664) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)Cc1ccn(C)n1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340053412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340053412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001340053412 none CCN(C(=O)Cc1ccn(C)n1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 17, 24, 28, 28, 43, 48, 48, 48, 48, 48, 10, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 43, 43, 48, 48, 48, 48, 48, 17, 17, 17, 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: 226 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340053412 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053412 Building ZINC001340053694 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340053694 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/665 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CCC(=O)N1C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340053694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340053694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340053694 none CCN(C(=O)[C@H]1CCC(=O)N1C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 32, 22, 32, 45, 46, 48, 48, 48, 48, 48, 48, 48, 11, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 48, 48, 48, 48, 48, 48, 48, 22, 22, 22, 11, 11, 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: 228 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/666 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/666' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CCC(=O)N1C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340053694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340053694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340053694 none CCN(C(=O)[C@H]1CCC(=O)N1C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 29, 20, 29, 37, 39, 43, 43, 43, 43, 43, 43, 43, 12, 20, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 43, 43, 43, 43, 43, 43, 43, 20, 20, 20, 12, 12, 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: 232 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340053694 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694 Building ZINC001340053694 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340053694 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 665) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@H]1CCC(=O)N1C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340053694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340053694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340053694 none CCN(C(=O)[C@H]1CCC(=O)N1C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 32, 22, 32, 45, 46, 48, 48, 48, 48, 48, 48, 48, 11, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 48, 48, 48, 48, 48, 48, 48, 22, 22, 22, 11, 11, 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: 228 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 666) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@H]1CCC(=O)N1C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340053694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340053694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340053694 none CCN(C(=O)[C@H]1CCC(=O)N1C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 29, 20, 29, 37, 39, 43, 43, 43, 43, 43, 43, 43, 12, 20, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 43, 43, 43, 43, 43, 43, 43, 20, 20, 20, 12, 12, 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: 232 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340053694 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340053694 Building ZINC001340054071 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340054071 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/667 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)c1c[nH]c(=O)cn1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340054071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340054071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340054071 none CCN(C(=O)c1c[nH]c(=O)cn1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 33, 27, 33, 42, 42, 44, 44, 44, 44, 44, 44, 44, 13, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 44, 44, 27, 27, 27, 13, 13, 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: 204 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/668 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/668' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)c1c[nH]c(=O)cn1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340054071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340054071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340054071 none CCN(C(=O)c1c[nH]c(=O)cn1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 26, 33, 43, 43, 46, 46, 46, 46, 46, 46, 46, 12, 26, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 46, 46, 26, 26, 26, 12, 12, 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: 192 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340054071 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071 Building ZINC001340054071 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340054071 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 667) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)c1c[nH]c(=O)cn1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340054071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340054071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340054071 none CCN(C(=O)c1c[nH]c(=O)cn1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 33, 27, 33, 42, 42, 44, 44, 44, 44, 44, 44, 44, 13, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 44, 44, 27, 27, 27, 13, 13, 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: 204 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 668) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)c1c[nH]c(=O)cn1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340054071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340054071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340054071 none CCN(C(=O)c1c[nH]c(=O)cn1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 26, 33, 43, 43, 46, 46, 46, 46, 46, 46, 46, 12, 26, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 46, 46, 26, 26, 26, 12, 12, 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: 192 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340054071 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340054071 Building ZINC001340059147 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340059147 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/669 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1nnn(C)c1C) `ZINC001340059147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340059147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340059147 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1nnn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 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, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 29, 29, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 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: 203 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/670 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1nnn(C)c1C) `ZINC001340059147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340059147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340059147 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1nnn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 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: [5, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 27, 47, 47, 47, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 27, 27, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 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: 188 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340059147 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147 Building ZINC001340059147 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340059147 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 669) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1nnn(C)c1C) `ZINC001340059147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340059147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340059147 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1nnn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 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, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 29, 29, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 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: 203 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 670) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1nnn(C)c1C) `ZINC001340059147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340059147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340059147 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1nnn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 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: [5, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 27, 47, 47, 47, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 27, 27, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 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: 188 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340059147 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340059147 Building ZINC001340066805 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340066805 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/671 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CN1CCOCC1) `ZINC001340066805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340066805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001340066805 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 15, 15, 15, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 15, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/672 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/672' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CN1CCOCC1) `ZINC001340066805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340066805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001340066805 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 16, 16, 16, 41, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 16, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340066805 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805 Building ZINC001340066805 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340066805 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 671) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CN1CCOCC1) `ZINC001340066805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340066805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001340066805 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 15, 15, 15, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 15, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 672) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CN1CCOCC1) `ZINC001340066805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340066805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001340066805 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 16, 16, 16, 41, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 16, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340066805 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340066805 Building ZINC001340074069 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340074069 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/673 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)C1CCOCC1) `ZINC001340074069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340074069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001340074069 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 11, 22, 25, 25, 17, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 25, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/674 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/674' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)C1CCOCC1) `ZINC001340074069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340074069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001340074069 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 18, 18, 26, 27, 27, 24, 38, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 26, 26, 27, 27, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 156 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340074069 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069 Building ZINC001340074069 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340074069 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 673) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)C1CCOCC1) `ZINC001340074069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340074069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001340074069 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 11, 22, 25, 25, 17, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 25, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 674) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)C1CCOCC1) `ZINC001340074069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340074069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001340074069 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 18, 18, 26, 27, 27, 24, 38, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 26, 26, 27, 27, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 156 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340074069 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074069 Building ZINC001340074093 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340074093 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/675 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(N)=O)C1CCOCC1) `ZINC001340074093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340074093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001340074093 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(N)=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 19, 19, 27, 28, 28, 28, 41, 41, 41, 41, 41, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 27, 27, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 161 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/676 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/676' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(N)=O)C1CCOCC1) `ZINC001340074093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340074093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001340074093 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(N)=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 11, 23, 26, 26, 17, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 26, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340074093 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093 Building ZINC001340074093 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340074093 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 675) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(N)=O)C1CCOCC1) `ZINC001340074093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340074093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001340074093 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(N)=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 19, 19, 27, 28, 28, 28, 41, 41, 41, 41, 41, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 27, 27, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 161 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 676) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(N)=O)C1CCOCC1) `ZINC001340074093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340074093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001340074093 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(N)=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 11, 23, 26, 26, 17, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 26, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340074093 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340074093 Building ZINC001340091080 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340091080 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/677 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)Cc1n[nH]c(C)n1) `ZINC001340091080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340091080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340091080 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)Cc1n[nH]c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 1, 8, 8, 6, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 11, 13, 13, 13, 28, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 13, 28, 28, 49, 49, 49] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/678 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)Cc1n[nH]c(C)n1) `ZINC001340091080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340091080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340091080 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)Cc1n[nH]c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 1, 8, 8, 6, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 9, 14, 14, 14, 25, 42, 42, 42, 42, 42, 42, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 14, 25, 25, 42, 42, 42] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340091080 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080 Building ZINC001340091080 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340091080 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 677) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)Cc1n[nH]c(C)n1) `ZINC001340091080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340091080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340091080 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)Cc1n[nH]c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 1, 8, 8, 6, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 11, 13, 13, 13, 28, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 13, 28, 28, 49, 49, 49] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 678) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)Cc1n[nH]c(C)n1) `ZINC001340091080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340091080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340091080 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)Cc1n[nH]c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 1, 8, 8, 6, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 9, 14, 14, 14, 25, 42, 42, 42, 42, 42, 42, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 14, 25, 25, 42, 42, 42] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340091080 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340091080 Building ZINC001340105231 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340105231 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/679 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@H]1CC(=O)N(C)C1) `ZINC001340105231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340105231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340105231 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 11, 25, 25, 36, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 25, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/680 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/680' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@H]1CC(=O)N(C)C1) `ZINC001340105231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340105231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340105231 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 8, 22, 22, 34, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340105231 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231 Building ZINC001340105231 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340105231 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 679) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@H]1CC(=O)N(C)C1) `ZINC001340105231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340105231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340105231 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 11, 25, 25, 36, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 25, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 680) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@H]1CC(=O)N(C)C1) `ZINC001340105231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340105231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340105231 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 8, 22, 22, 34, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340105231 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105231 Building ZINC001340105233 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340105233 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/681 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CC(=O)N(C)C1) `ZINC001340105233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340105233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340105233 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 10, 22, 22, 33, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 22, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/682 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/682' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CC(=O)N(C)C1) `ZINC001340105233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340105233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340105233 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 10, 21, 21, 34, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 21, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340105233 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233 Building ZINC001340105233 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340105233 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 681) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CC(=O)N(C)C1) `ZINC001340105233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340105233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340105233 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 10, 22, 22, 33, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 22, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 682) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CC(=O)N(C)C1) `ZINC001340105233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340105233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340105233 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 10, 21, 21, 34, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 21, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340105233 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340105233 Building ZINC001340153184 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340153184 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/683 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CCC(=O)N1C) `ZINC001340153184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340153184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340153184 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 17, 36, 36, 37, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 36, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/684 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/684' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CCC(=O)N1C) `ZINC001340153184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340153184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340153184 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 15, 37, 37, 41, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 37, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340153184 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184 Building ZINC001340153184 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340153184 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 683) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CCC(=O)N1C) `ZINC001340153184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340153184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340153184 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 17, 36, 36, 37, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 36, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 684) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CCC(=O)N1C) `ZINC001340153184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340153184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340153184 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 15, 37, 37, 41, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 37, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340153184 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340153184 Building ZINC001340163055 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340163055 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/685 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1c[nH]c(=O)cn1) `ZINC001340163055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340163055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001340163055 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 31, 31, 49, 49, 49] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 211 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/686 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/686' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1c[nH]c(=O)cn1) `ZINC001340163055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340163055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001340163055 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 29, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 29, 29, 49, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340163055 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055 Building ZINC001340163055 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340163055 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 685) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1c[nH]c(=O)cn1) `ZINC001340163055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340163055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001340163055 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 31, 31, 49, 49, 49] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 211 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 686) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1c[nH]c(=O)cn1) `ZINC001340163055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340163055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001340163055 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 29, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 29, 29, 49, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340163055 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163055 Building ZINC001340163820 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340163820 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/687 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)C(=O)NCC1CC1) `ZINC001340163820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340163820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340163820 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 6, 11, 11, 11, 14, 10, 10, 33, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 11, 14, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/688 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/688' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)C(=O)NCC1CC1) `ZINC001340163820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340163820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340163820 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 5, 10, 10, 10, 13, 8, 8, 28, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 10, 13, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340163820 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820 Building ZINC001340163820 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340163820 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 687) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)C(=O)NCC1CC1) `ZINC001340163820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340163820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340163820 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 6, 11, 11, 11, 14, 10, 10, 33, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 11, 14, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 688) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)C(=O)NCC1CC1) `ZINC001340163820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340163820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001340163820 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 5, 10, 10, 10, 13, 8, 8, 28, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 10, 13, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340163820 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340163820 Building ZINC001340191733 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340191733 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/689 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CCc1cnn[nH]1) `ZINC001340191733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340191733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340191733 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 8, 8, 8, 28, 38, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 8, 28, 28, 38, 38, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/690 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/690' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CCc1cnn[nH]1) `ZINC001340191733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340191733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340191733 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 7, 11, 11, 11, 35, 39, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 35, 35, 39, 39, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340191733 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733 Building ZINC001340191733 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340191733 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 689) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CCc1cnn[nH]1) `ZINC001340191733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340191733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340191733 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 8, 8, 8, 28, 38, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 8, 28, 28, 38, 38, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 690) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CCc1cnn[nH]1) `ZINC001340191733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340191733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340191733 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)CNC(=O)CCc1cnn[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 7, 11, 11, 11, 35, 39, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 35, 35, 39, 39, 50] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340191733 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340191733 Building ZINC001340203190 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340203190 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/691 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCCC[C@@H]1CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340203190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340203190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001340203190 none CC(=O)NCC(=O)N1CCCC[C@@H]1CN(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 12, 20, 12, 12, 12, 12, 12, 7, 12, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 42, 42, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 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: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/692 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/692' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCCC[C@@H]1CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340203190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340203190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001340203190 none CC(=O)NCC(=O)N1CCCC[C@@H]1CN(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 19, 10, 19, 10, 10, 10, 10, 10, 5, 10, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 43, 43, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340203190 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190 Building ZINC001340203190 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340203190 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 691) grep: /scratch/xiaobo/2379/xbv-8058097.48/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(=O)NCC(=O)N1CCCC[C@@H]1CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340203190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340203190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001340203190 none CC(=O)NCC(=O)N1CCCC[C@@H]1CN(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 12, 20, 12, 12, 12, 12, 12, 7, 12, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 42, 42, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 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: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 692) grep: /scratch/xiaobo/2379/xbv-8058097.48/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(=O)NCC(=O)N1CCCC[C@@H]1CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340203190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340203190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001340203190 none CC(=O)NCC(=O)N1CCCC[C@@H]1CN(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 19, 10, 19, 10, 10, 10, 10, 10, 5, 10, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 43, 43, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340203190 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340203190 Building ZINC001340225352 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340225352 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/693 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCCN1C(=O)c1cn(C)nn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340225352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340225352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340225352 none CN(C[C@H]1CCCCN1C(=O)c1cn(C)nn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 8, 16, 16, 16, 16, 16, 16, 16, 37, 37, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/694 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/694' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCCN1C(=O)c1cn(C)nn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340225352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340225352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340225352 none CN(C[C@H]1CCCCN1C(=O)c1cn(C)nn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 18, 18, 18, 18, 18, 18, 18, 39, 39, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340225352 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352 Building ZINC001340225352 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340225352 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 693) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCCN1C(=O)c1cn(C)nn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340225352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340225352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340225352 none CN(C[C@H]1CCCCN1C(=O)c1cn(C)nn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 8, 16, 16, 16, 16, 16, 16, 16, 37, 37, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 694) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCCN1C(=O)c1cn(C)nn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340225352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340225352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340225352 none CN(C[C@H]1CCCCN1C(=O)c1cn(C)nn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 18, 18, 18, 18, 18, 18, 18, 39, 39, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340225352 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340225352 Building ZINC001340328167 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340328167 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/695 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N2CC=C(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)nn1) `ZINC001340328167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340328167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340328167 none Cn1cc(C(=O)N2CC=C(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 38, 49, 38, 38, 33, 16, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38] 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/696 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/696' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N2CC=C(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)nn1) `ZINC001340328167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340328167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340328167 none Cn1cc(C(=O)N2CC=C(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 38, 49, 38, 38, 34, 17, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38] 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: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340328167 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167 Building ZINC001340328167 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340328167 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 695) grep: /scratch/xiaobo/2379/xbv-8058097.48/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(=O)N2CC=C(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)nn1) `ZINC001340328167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340328167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340328167 none Cn1cc(C(=O)N2CC=C(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 38, 49, 38, 38, 33, 16, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38] 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 696) grep: /scratch/xiaobo/2379/xbv-8058097.48/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(=O)N2CC=C(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)nn1) `ZINC001340328167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340328167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340328167 none Cn1cc(C(=O)N2CC=C(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 38, 49, 38, 38, 34, 17, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38] 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: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340328167 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340328167 Building ZINC001340421257 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340421257 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/697 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/697' -> `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(CCNC(=O)c2nc[nH]n2)CC1) `ZINC001340421257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340421257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340421257 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CCNC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 17, 24, 35, 35, 35, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 24, 24, 35, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/698 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/698' -> `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(CCNC(=O)c2nc[nH]n2)CC1) `ZINC001340421257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340421257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340421257 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CCNC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 18, 25, 35, 35, 35, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 25, 25, 35, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340421257 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257 Building ZINC001340421257 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340421257 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 697) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CCNC(=O)c2nc[nH]n2)CC1) `ZINC001340421257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340421257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340421257 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC=C(CCNC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 17, 24, 35, 35, 35, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 24, 24, 35, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 698) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CCNC(=O)c2nc[nH]n2)CC1) `ZINC001340421257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340421257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340421257 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC=C(CCNC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 18, 25, 35, 35, 35, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 25, 25, 35, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340421257 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340421257 Building ZINC001340482016 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340482016 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/699 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)C(N)=O)CCc1ccccc1) `ZINC001340482016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340482016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001340482016 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)C(N)=O)CCc1ccccc1 NO_LONG_NAME dock 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.am', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 11, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 13, 28, 28, 28, 42, 43, 4, 9, 9, 12, 12, 10, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 13, 13, 28, 43, 42, 9, 9, 9, 9, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/700 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/700' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)C(N)=O)CCc1ccccc1) `ZINC001340482016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340482016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001340482016 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)C(N)=O)CCc1ccccc1 NO_LONG_NAME dock 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.am', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 11, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 12, 27, 27, 27, 42, 43, 4, 8, 8, 11, 11, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 12, 12, 27, 43, 42, 8, 8, 8, 8, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340482016 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016 Building ZINC001340482016 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340482016 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 699) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)C(N)=O)CCc1ccccc1) `ZINC001340482016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340482016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001340482016 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)C(N)=O)CCc1ccccc1 NO_LONG_NAME dock 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.am', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 11, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 13, 28, 28, 28, 42, 43, 4, 9, 9, 12, 12, 10, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 13, 13, 28, 43, 42, 9, 9, 9, 9, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 700) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)C(N)=O)CCc1ccccc1) `ZINC001340482016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340482016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001340482016 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)C(N)=O)CCc1ccccc1 NO_LONG_NAME dock 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.am', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 11, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 12, 27, 27, 27, 42, 43, 4, 8, 8, 11, 11, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 12, 12, 27, 43, 42, 8, 8, 8, 8, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340482016 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340482016 Building ZINC001340488974 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340488974 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/701 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NCCC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001340488974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340488974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340488974 none CC(=O)NCC(=O)NCCC1(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 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, 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] 0 hydrogens need rotated 50 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, 22, 22, 22, 19, 19, 19, 15, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 19, 19, 50, 50, 50, 50, 46, 46, 22, 19, 19, 19, 19, 15, 15, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/702 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NCCC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001340488974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340488974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340488974 none CC(=O)NCC(=O)NCCC1(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 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, 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] 0 hydrogens need rotated 50 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, 21, 21, 21, 19, 19, 19, 16, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 19, 19, 50, 50, 50, 50, 46, 46, 21, 19, 19, 19, 19, 16, 16, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340488974 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974 Building ZINC001340488974 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340488974 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 701) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(=O)NCC(=O)NCCC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001340488974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340488974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340488974 none CC(=O)NCC(=O)NCCC1(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 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, 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] 0 hydrogens need rotated 50 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, 22, 22, 22, 19, 19, 19, 15, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 19, 19, 50, 50, 50, 50, 46, 46, 22, 19, 19, 19, 19, 15, 15, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 702) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(=O)NCC(=O)NCCC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001340488974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340488974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340488974 none CC(=O)NCC(=O)NCCC1(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 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, 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] 0 hydrogens need rotated 50 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, 21, 21, 21, 19, 19, 19, 16, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 19, 19, 50, 50, 50, 50, 46, 46, 21, 19, 19, 19, 19, 16, 16, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340488974 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340488974 Building ZINC001340513472 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340513472 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/703 `/scratch/xiaobo/2379/xbv-8058097.48/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)NCCC1(CNC(=O)C2=COCCO2)CC1) `ZINC001340513472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340513472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001340513472 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)C2=COCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 10, 16, 33, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 10, 10, 33, 33, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/704 `/scratch/xiaobo/2379/xbv-8058097.48/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)NCCC1(CNC(=O)C2=COCCO2)CC1) `ZINC001340513472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340513472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001340513472 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)C2=COCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 10, 16, 32, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 10, 10, 32, 32, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340513472 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472 Building ZINC001340513472 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340513472 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 703) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)NCCC1(CNC(=O)C2=COCCO2)CC1) `ZINC001340513472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340513472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001340513472 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)C2=COCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 10, 16, 33, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 10, 10, 33, 33, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 704) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)NCCC1(CNC(=O)C2=COCCO2)CC1) `ZINC001340513472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340513472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001340513472 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)C2=COCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 10, 16, 32, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 10, 10, 32, 32, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340513472 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513472 Building ZINC001340513507 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340513507 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/705 `/scratch/xiaobo/2379/xbv-8058097.48/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)NCCC1(CNC(=O)C2(C(N)=O)CC2)CC1) `ZINC001340513507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340513507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340513507 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)C2(C(N)=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 15, 21, 36, 36, 36, 49, 50, 50, 49, 49, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 21, 21, 36, 50, 50, 49, 49, 49, 49, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/706 `/scratch/xiaobo/2379/xbv-8058097.48/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)NCCC1(CNC(=O)C2(C(N)=O)CC2)CC1) `ZINC001340513507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340513507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340513507 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)C2(C(N)=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 14, 22, 39, 39, 39, 48, 50, 50, 48, 48, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 22, 22, 39, 50, 50, 48, 48, 48, 48, 14, 14, 14, 14] 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: 178 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340513507 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507 Building ZINC001340513507 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340513507 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 705) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)NCCC1(CNC(=O)C2(C(N)=O)CC2)CC1) `ZINC001340513507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340513507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340513507 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)C2(C(N)=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 15, 21, 36, 36, 36, 49, 50, 50, 49, 49, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 21, 21, 36, 50, 50, 49, 49, 49, 49, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 706) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)NCCC1(CNC(=O)C2(C(N)=O)CC2)CC1) `ZINC001340513507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340513507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340513507 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)C2(C(N)=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 14, 22, 39, 39, 39, 48, 50, 50, 48, 48, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 22, 22, 39, 50, 50, 48, 48, 48, 48, 14, 14, 14, 14] 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: 178 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340513507 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513507 Building ZINC001340513880 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340513880 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/707 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)Cc2ncc[nH]2)CC1) `ZINC001340513880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340513880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001340513880 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)Cc2ncc[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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 11, 15, 22, 33, 33, 33, 49, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 12, 12, 22, 22, 33, 49, 49, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 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: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/708 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/708' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)Cc2ncc[nH]2)CC1) `ZINC001340513880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340513880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001340513880 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)Cc2ncc[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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 12, 16, 22, 33, 33, 33, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 13, 13, 22, 22, 33, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340513880 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880 Building ZINC001340513880 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340513880 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 707) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)Cc2ncc[nH]2)CC1) `ZINC001340513880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340513880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001340513880 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)Cc2ncc[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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 11, 15, 22, 33, 33, 33, 49, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 12, 12, 22, 22, 33, 49, 49, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 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: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 708) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)Cc2ncc[nH]2)CC1) `ZINC001340513880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340513880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001340513880 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)Cc2ncc[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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 12, 16, 22, 33, 33, 33, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 13, 13, 22, 22, 33, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340513880 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513880 Building ZINC001340513895 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340513895 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/709 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCC2(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)c1N) `ZINC001340513895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340513895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340513895 none Cn1ncc(C(=O)NCC2(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 8, 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, 6, 6] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 39, 30, 21, 14, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50, 50, 50, 50, 39, 30, 30, 14, 14, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/710 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/710' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCC2(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)c1N) `ZINC001340513895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340513895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340513895 none Cn1ncc(C(=O)NCC2(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 8, 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, 6, 6] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 42, 42, 33, 25, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 42, 33, 33, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340513895 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895 Building ZINC001340513895 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340513895 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 709) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1ncc(C(=O)NCC2(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)c1N) `ZINC001340513895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340513895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340513895 none Cn1ncc(C(=O)NCC2(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 8, 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, 6, 6] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 39, 30, 21, 14, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50, 50, 50, 50, 39, 30, 30, 14, 14, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 710) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1ncc(C(=O)NCC2(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)c1N) `ZINC001340513895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340513895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340513895 none Cn1ncc(C(=O)NCC2(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 8, 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, 6, 6] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 42, 42, 33, 25, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 42, 33, 33, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340513895 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513895 Building ZINC001340513920 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340513920 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/711 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)NCC2(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001340513920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340513920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340513920 none CCn1ncc(C(=O)NCC2(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 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, 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, 30, 30, 30, 30, 30, 30, 30, 23, 14, 7, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 30, 50, 50, 50, 50, 50, 30, 30, 23, 23, 7, 7, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/712 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/712' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)NCC2(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001340513920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340513920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340513920 none CCn1ncc(C(=O)NCC2(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 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, 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, 29, 29, 29, 29, 29, 29, 29, 22, 15, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 29, 50, 50, 50, 50, 50, 29, 29, 22, 22, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340513920 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920 Building ZINC001340513920 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340513920 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 711) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1ncc(C(=O)NCC2(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001340513920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340513920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340513920 none CCn1ncc(C(=O)NCC2(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 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, 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, 30, 30, 30, 30, 30, 30, 30, 23, 14, 7, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 30, 50, 50, 50, 50, 50, 30, 30, 23, 23, 7, 7, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 712) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCn1ncc(C(=O)NCC2(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001340513920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340513920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340513920 none CCn1ncc(C(=O)NCC2(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 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, 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, 29, 29, 29, 29, 29, 29, 29, 22, 15, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 29, 50, 50, 50, 50, 50, 29, 29, 22, 22, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340513920 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340513920 Building ZINC001340514540 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340514540 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/713 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(=O)NCC2(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1) `ZINC001340514540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340514540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340514540 none Cc1nc(CC(=O)NCC2(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 35, 35, 24, 19, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 50, 50, 50, 50, 50, 50, 40, 40, 35, 24, 24, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 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: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/714 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/714' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(=O)NCC2(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1) `ZINC001340514540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340514540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340514540 none Cc1nc(CC(=O)NCC2(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 35, 35, 25, 20, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 50, 39, 39, 35, 25, 25, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20] 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: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340514540 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540 Building ZINC001340514540 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340514540 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 713) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(CC(=O)NCC2(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1) `ZINC001340514540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340514540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340514540 none Cc1nc(CC(=O)NCC2(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 35, 35, 24, 19, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 50, 50, 50, 50, 50, 50, 40, 40, 35, 24, 24, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 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: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 714) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(CC(=O)NCC2(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1) `ZINC001340514540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340514540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340514540 none Cc1nc(CC(=O)NCC2(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 35, 35, 25, 20, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 50, 39, 39, 35, 25, 25, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20] 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: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340514540 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340514540 Building ZINC001340515087 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340515087 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/715 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NCCC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001340515087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340515087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001340515087 none CCNC(=O)CC(=O)NCCC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 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, 31, 31, 31, 31, 17, 17, 17, 14, 14, 14, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 31, 31, 31, 17, 14, 14, 14, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 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: 238 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/716 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/716' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NCCC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001340515087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340515087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001340515087 none CCNC(=O)CC(=O)NCCC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 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, 34, 34, 31, 34, 15, 15, 15, 13, 12, 11, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 34, 31, 31, 15, 13, 13, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 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: 232 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340515087 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087 Building ZINC001340515087 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340515087 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 715) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCNC(=O)CC(=O)NCCC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001340515087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340515087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001340515087 none CCNC(=O)CC(=O)NCCC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 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, 31, 31, 31, 31, 17, 17, 17, 14, 14, 14, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 31, 31, 31, 17, 14, 14, 14, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 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: 238 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 716) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCNC(=O)CC(=O)NCCC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001340515087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340515087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001340515087 none CCNC(=O)CC(=O)NCCC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 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, 34, 34, 31, 34, 15, 15, 15, 13, 12, 11, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 34, 31, 31, 15, 13, 13, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 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: 232 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340515087 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515087 Building ZINC001340515712 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340515712 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/717 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NCCC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001340515712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340515712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340515712 none C[C@H](NC(N)=O)C(=O)NCCC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 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, 4, 7, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 50, 50, 50, 50, 50, 34, 34, 32, 27, 24, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 34, 32, 32, 27, 27, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/718 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/718' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NCCC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001340515712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340515712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340515712 none C[C@H](NC(N)=O)C(=O)NCCC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 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, 4, 7, 4, 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, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 30, 30, 28, 23, 19, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 50, 50, 50, 50, 50, 50, 30, 28, 28, 23, 23, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340515712 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712 Building ZINC001340515712 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340515712 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 717) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NCCC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001340515712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340515712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340515712 none C[C@H](NC(N)=O)C(=O)NCCC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 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, 4, 7, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 50, 50, 50, 50, 50, 34, 34, 32, 27, 24, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 34, 32, 32, 27, 27, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 718) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NCCC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001340515712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340515712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340515712 none C[C@H](NC(N)=O)C(=O)NCCC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 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, 4, 7, 4, 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, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 30, 30, 28, 23, 19, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 50, 50, 50, 50, 50, 50, 30, 28, 28, 23, 23, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340515712 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340515712 Building ZINC001340528348 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340528348 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/719 `/scratch/xiaobo/2379/xbv-8058097.48/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)NCC1(CCNC(=O)CCn2ccnn2)CC1) `ZINC001340528348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340528348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340528348 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(CCNC(=O)CCn2ccnn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 15, 15, 19, 19, 19, 40, 45, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 19, 40, 40, 45, 45, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/720 `/scratch/xiaobo/2379/xbv-8058097.48/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)NCC1(CCNC(=O)CCn2ccnn2)CC1) `ZINC001340528348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340528348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340528348 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(CCNC(=O)CCn2ccnn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 15, 15, 20, 20, 20, 41, 45, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 20, 41, 41, 45, 45, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340528348 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348 Building ZINC001340528348 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340528348 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 719) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)NCC1(CCNC(=O)CCn2ccnn2)CC1) `ZINC001340528348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340528348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340528348 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(CCNC(=O)CCn2ccnn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 15, 15, 19, 19, 19, 40, 45, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 19, 40, 40, 45, 45, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 720) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)NCC1(CCNC(=O)CCn2ccnn2)CC1) `ZINC001340528348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340528348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340528348 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(CCNC(=O)CCn2ccnn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 15, 15, 20, 20, 20, 41, 45, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 20, 41, 41, 45, 45, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340528348 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340528348 Building ZINC001340551577 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340551577 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/721 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCC2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001340551577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340551577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340551577 none Cn1ncc(C(=O)NCCC2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 34, 27, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 42, 42, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/722 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCC2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001340551577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340551577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340551577 none Cn1ncc(C(=O)NCCC2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 34, 27, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 42, 42, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340551577 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577 Building ZINC001340551577 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340551577 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 721) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1ncc(C(=O)NCCC2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001340551577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340551577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340551577 none Cn1ncc(C(=O)NCCC2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 34, 27, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 42, 42, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 722) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1ncc(C(=O)NCCC2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001340551577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340551577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001340551577 none Cn1ncc(C(=O)NCCC2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 34, 27, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 42, 42, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340551577 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340551577 Building ZINC001340592221 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340592221 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/723 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(CCNC(=O)Cn2cncn2)CC1) `ZINC001340592221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340592221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340592221 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(CCNC(=O)Cn2cncn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 9, 10, 10, 11, 11, 11, 36, 50, 50, 50, 50, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 10, 10, 10, 10, 11, 36, 36, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/724 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/724' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(CCNC(=O)Cn2cncn2)CC1) `ZINC001340592221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340592221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340592221 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(CCNC(=O)Cn2cncn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 10, 10, 13, 13, 13, 37, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 13, 37, 37, 50, 50, 7, 7, 7, 7] 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: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340592221 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221 Building ZINC001340592221 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340592221 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 723) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(CCNC(=O)Cn2cncn2)CC1) `ZINC001340592221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340592221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340592221 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(CCNC(=O)Cn2cncn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 9, 10, 10, 11, 11, 11, 36, 50, 50, 50, 50, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 10, 10, 10, 10, 11, 36, 36, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 724) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(CCNC(=O)Cn2cncn2)CC1) `ZINC001340592221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340592221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340592221 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(CCNC(=O)Cn2cncn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 10, 10, 13, 13, 13, 37, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 13, 37, 37, 50, 50, 7, 7, 7, 7] 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: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340592221 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340592221 Building ZINC001340602975 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340602975 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/725 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)N3CCOCC3)CC2)c1) `ZINC001340602975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340602975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001340602975 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)N3CCOCC3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 11, 24, 24, 24, 24, 27, 27, 27, 27, 27, 27, 27, 24, 24, 2, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 27, 27, 27, 27, 27, 27, 27, 27, 24, 24, 24, 24, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/726 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)N3CCOCC3)CC2)c1) `ZINC001340602975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340602975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001340602975 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)N3CCOCC3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 14, 23, 24, 24, 24, 26, 26, 26, 26, 26, 26, 26, 24, 24, 2, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 26, 26, 26, 26, 26, 26, 26, 26, 24, 24, 24, 24, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340602975 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975 Building ZINC001340602975 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340602975 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 725) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)N3CCOCC3)CC2)c1) `ZINC001340602975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340602975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001340602975 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)N3CCOCC3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 11, 24, 24, 24, 24, 27, 27, 27, 27, 27, 27, 27, 24, 24, 2, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 27, 27, 27, 27, 27, 27, 27, 27, 24, 24, 24, 24, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 726) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)N3CCOCC3)CC2)c1) `ZINC001340602975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340602975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001340602975 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)N3CCOCC3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 14, 23, 24, 24, 24, 26, 26, 26, 26, 26, 26, 26, 24, 24, 2, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 26, 26, 26, 26, 26, 26, 26, 26, 24, 24, 24, 24, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340602975 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340602975 Building ZINC001340608698 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340608698 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/727 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340608698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608698 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 6, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/728 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340608698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608698 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340608698 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698 Building ZINC001340608698 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340608698 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 727) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340608698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608698 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 6, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 728) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340608698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608698 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340608698 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608698 Building ZINC001340608699 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340608699 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/729 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340608699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608699 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/730 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/730' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340608699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608699 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 5, 5, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340608699 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699 Building ZINC001340608699 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340608699 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 729) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340608699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608699 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 730) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340608699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608699 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 5, 5, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340608699 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608699 Building ZINC001340608700 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340608700 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/731 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340608700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608700 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12, 12, 12, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/732 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340608700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608700 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340608700 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700 Building ZINC001340608700 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340608700 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 731) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340608700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608700 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12, 12, 12, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 732) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340608700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608700 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340608700 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608700 Building ZINC001340608701 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340608701 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/733 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340608701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608701 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 6, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/734 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/734' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340608701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608701 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340608701 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701 Building ZINC001340608701 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340608701 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 733) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340608701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608701 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 6, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 734) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1) `ZINC001340608701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340608701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340608701 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]3(CCNC3)Oc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 10, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340608701 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340608701 Building ZINC001340654464 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340654464 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/735 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340654464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340654464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340654464 none C[C@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 14, 17, 28, 28, 28, 36, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 15, 16, 16, 19, 19, 28, 36, 36, 50, 2, 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: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/736 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/736' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340654464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340654464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340654464 none C[C@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 14, 16, 18, 28, 29, 28, 33, 49, 49, 49, 49, 49, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 14, 14, 14, 17, 17, 19, 19, 29, 33, 33, 49, 3, 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340654464 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464 Building ZINC001340654464 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340654464 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 735) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340654464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340654464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340654464 none C[C@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 14, 17, 28, 28, 28, 36, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 15, 16, 16, 19, 19, 28, 36, 36, 50, 2, 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: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 736) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340654464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340654464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340654464 none C[C@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 14, 16, 18, 28, 29, 28, 33, 49, 49, 49, 49, 49, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 14, 14, 14, 17, 17, 19, 19, 29, 33, 33, 49, 3, 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340654464 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654464 Building ZINC001340654466 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340654466 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/737 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340654466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340654466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340654466 none C[C@@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 14, 16, 18, 29, 30, 29, 34, 49, 49, 49, 49, 49, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 14, 14, 14, 17, 17, 19, 19, 30, 34, 34, 50, 3, 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: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/738 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/738' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340654466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340654466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340654466 none C[C@@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 14, 17, 28, 28, 28, 36, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 15, 14, 16, 16, 19, 19, 28, 36, 36, 50, 2, 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: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340654466 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466 Building ZINC001340654466 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340654466 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 737) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340654466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340654466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340654466 none C[C@@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 14, 16, 18, 29, 30, 29, 34, 49, 49, 49, 49, 49, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 14, 14, 14, 17, 17, 19, 19, 30, 34, 34, 50, 3, 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: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 738) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340654466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340654466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001340654466 none C[C@@H](CCCCNC(=O)Cc1nc[nH]n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 14, 17, 28, 28, 28, 36, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 15, 14, 16, 16, 19, 19, 28, 36, 36, 50, 2, 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: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340654466 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340654466 Building ZINC001340792896 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340792896 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/739 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1) `ZINC001340792896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340792896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340792896 none C[C@H](CCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 23, 23, 23, 46, 50, 50, 50, 50, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 46, 46, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/740 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/740' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1) `ZINC001340792896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340792896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340792896 none C[C@H](CCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 16, 12, 12, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 22, 22, 22, 44, 50, 50, 50, 50, 16, 16, 16, 12, 12, 12, 12, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 44, 44, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340792896 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896 Building ZINC001340792896 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340792896 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 739) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1) `ZINC001340792896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340792896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340792896 none C[C@H](CCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 23, 23, 23, 46, 50, 50, 50, 50, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 46, 46, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 740) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1) `ZINC001340792896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340792896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340792896 none C[C@H](CCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 16, 12, 12, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 22, 22, 22, 44, 50, 50, 50, 50, 16, 16, 16, 12, 12, 12, 12, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 44, 44, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340792896 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792896 Building ZINC001340792898 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340792898 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/741 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1) `ZINC001340792898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340792898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340792898 none C[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 15, 12, 12, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 21, 21, 21, 44, 50, 50, 50, 50, 15, 15, 15, 12, 12, 12, 12, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 44, 44, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/742 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/742' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1) `ZINC001340792898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340792898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340792898 none C[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 10, 10, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 23, 23, 23, 46, 50, 50, 50, 50, 15, 15, 15, 10, 10, 10, 10, 10, 10, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 46, 46, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340792898 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898 Building ZINC001340792898 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340792898 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 741) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1) `ZINC001340792898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340792898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340792898 none C[C@@H](CCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 15, 12, 12, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 21, 21, 21, 44, 50, 50, 50, 50, 15, 15, 15, 12, 12, 12, 12, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 44, 44, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 742) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1) `ZINC001340792898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340792898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001340792898 none C[C@@H](CCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 10, 10, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 23, 23, 23, 46, 50, 50, 50, 50, 15, 15, 15, 10, 10, 10, 10, 10, 10, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 46, 46, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340792898 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340792898 Building ZINC001340831749 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340831749 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/743 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CN2CCNC2=O)CC1) `ZINC001340831749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340831749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001340831749 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CN2CCNC2=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 24, 35, 35, 35, 35, 35, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 24, 24, 35, 35, 35, 35, 35, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/744 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CN2CCNC2=O)CC1) `ZINC001340831749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340831749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001340831749 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CN2CCNC2=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 28, 38, 38, 38, 38, 38, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 28, 28, 38, 38, 38, 38, 38, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340831749 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749 Building ZINC001340831749 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340831749 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 743) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CN2CCNC2=O)CC1) `ZINC001340831749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340831749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001340831749 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CN2CCNC2=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 24, 35, 35, 35, 35, 35, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 24, 24, 35, 35, 35, 35, 35, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 744) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CN2CCNC2=O)CC1) `ZINC001340831749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340831749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001340831749 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CN2CCNC2=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 28, 38, 38, 38, 38, 38, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 28, 28, 38, 38, 38, 38, 38, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340831749 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340831749 Building ZINC001340848783 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340848783 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/745 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001340848783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340848783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001340848783 none COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 17, 43, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 43, 43, 43, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/746 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001340848783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340848783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001340848783 none COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 19, 43, 19, 19, 19, 19, 19, 19, 19, 19, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 43, 43, 43, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340848783 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783 Building ZINC001340848783 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340848783 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 745) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001340848783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340848783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001340848783 none COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 17, 43, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 43, 43, 43, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 746) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001340848783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340848783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001340848783 none COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 19, 43, 19, 19, 19, 19, 19, 19, 19, 19, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 43, 43, 43, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340848783 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848783 Building ZINC001340848781 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340848781 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/747 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001340848781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340848781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001340848781 none COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 15, 34, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/748 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/748' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001340848781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340848781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001340848781 none COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 17, 44, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 44, 44, 44, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340848781 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781 Building ZINC001340848781 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340848781 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 747) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001340848781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340848781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001340848781 none COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 15, 34, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 748) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001340848781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340848781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001340848781 none COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 17, 44, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 44, 44, 44, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340848781 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340848781 Building ZINC001340875964 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340875964 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/749 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340875964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340875964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875964 none C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 23, 23, 34, 50, 50, 50, 50, 50, 20, 20, 13, 20, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 34, 34, 50, 20, 20, 20, 20, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/750 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340875964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340875964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875964 none C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 21, 21, 33, 50, 50, 50, 50, 50, 17, 17, 13, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 33, 33, 50, 17, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 165 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340875964 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964 Building ZINC001340875964 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340875964 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 749) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340875964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340875964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875964 none C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 23, 23, 34, 50, 50, 50, 50, 50, 20, 20, 13, 20, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 34, 34, 50, 20, 20, 20, 20, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 750) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340875964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340875964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875964 none C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 21, 21, 33, 50, 50, 50, 50, 50, 17, 17, 13, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 33, 33, 50, 17, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 165 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340875964 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875964 Building ZINC001340875965 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340875965 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/751 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340875965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340875965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875965 none C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 26, 26, 36, 50, 50, 50, 50, 50, 19, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 36, 36, 50, 19, 19, 19, 19, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/752 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340875965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340875965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875965 none C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 26, 26, 35, 50, 50, 50, 50, 50, 20, 20, 12, 20, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 35, 35, 50, 20, 20, 20, 20, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340875965 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965 Building ZINC001340875965 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340875965 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 751) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340875965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340875965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875965 none C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 26, 26, 36, 50, 50, 50, 50, 50, 19, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 36, 36, 50, 19, 19, 19, 19, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 752) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340875965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340875965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875965 none C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 26, 26, 35, 50, 50, 50, 50, 50, 20, 20, 12, 20, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 35, 35, 50, 20, 20, 20, 20, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340875965 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875965 Building ZINC001340875966 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340875966 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/753 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340875966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340875966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875966 none C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 16, 16, 30, 50, 50, 50, 50, 50, 11, 11, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 50, 11, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/754 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340875966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340875966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875966 none C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 16, 16, 29, 50, 50, 50, 50, 50, 12, 12, 9, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 29, 29, 50, 12, 12, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340875966 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966 Building ZINC001340875966 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340875966 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 753) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340875966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340875966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875966 none C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 16, 16, 30, 50, 50, 50, 50, 50, 11, 11, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 50, 11, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 754) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340875966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340875966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875966 none C[C@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@H]1CNC(=O)[C@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 16, 16, 29, 50, 50, 50, 50, 50, 12, 12, 9, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 29, 29, 50, 12, 12, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340875966 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875966 Building ZINC001340875967 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340875967 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/755 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340875967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340875967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875967 none C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 15, 15, 29, 50, 50, 50, 50, 50, 12, 12, 9, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 29, 29, 50, 12, 12, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 150 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/756 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/756' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340875967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340875967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875967 none C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 16, 16, 30, 50, 50, 50, 50, 50, 11, 11, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 50, 11, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340875967 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967 Building ZINC001340875967 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340875967 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 755) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001340875967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340875967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875967 none C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 15, 15, 29, 50, 50, 50, 50, 50, 12, 12, 9, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 29, 29, 50, 12, 12, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 150 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 756) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001340875967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340875967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001340875967 none C[C@@H]1CN(C(=O)Cc2nc[nH]n2)CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 16, 16, 30, 50, 50, 50, 50, 50, 11, 11, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 50, 11, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340875967 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340875967 Building ZINC001340899094 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340899094 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/757 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001340899094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340899094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001340899094 none CC(=O)N[C@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 50, 50, 14, 30, 14, 14, 14, 14, 14, 14, 4, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/758 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/758' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001340899094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340899094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001340899094 none CC(=O)N[C@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 50, 11, 32, 11, 11, 11, 11, 11, 11, 4, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340899094 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094 Building ZINC001340899094 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340899094 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 757) grep: /scratch/xiaobo/2379/xbv-8058097.48/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(=O)N[C@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001340899094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340899094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001340899094 none CC(=O)N[C@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 50, 50, 14, 30, 14, 14, 14, 14, 14, 14, 4, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 758) grep: /scratch/xiaobo/2379/xbv-8058097.48/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(=O)N[C@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001340899094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340899094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001340899094 none CC(=O)N[C@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 50, 11, 32, 11, 11, 11, 11, 11, 11, 4, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340899094 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899094 Building ZINC001340899096 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340899096 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/759 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001340899096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340899096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001340899096 none CC(=O)N[C@@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 25, 48, 48, 10, 25, 10, 10, 10, 10, 10, 10, 3, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 48, 48, 48, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/760 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001340899096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340899096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001340899096 none CC(=O)N[C@@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 26, 47, 47, 9, 26, 9, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 47, 47, 47, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340899096 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096 Building ZINC001340899096 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340899096 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 759) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(=O)N[C@@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001340899096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340899096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001340899096 none CC(=O)N[C@@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 25, 48, 48, 10, 25, 10, 10, 10, 10, 10, 10, 3, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 48, 48, 48, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 760) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(=O)N[C@@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001340899096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340899096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001340899096 none CC(=O)N[C@@H](C)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 26, 47, 47, 9, 26, 9, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 47, 47, 47, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340899096 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899096 Building ZINC001340899825 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340899825 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/761 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1NC(=O)C[C@]12CCNC2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001340899825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340899825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001340899825 none O=C(N1NC(=O)C[C@]12CCNC2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 15, 15, 10, 15, 15, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/762 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1NC(=O)C[C@]12CCNC2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001340899825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340899825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001340899825 none O=C(N1NC(=O)C[C@]12CCNC2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 10, 10, 10, 10, 13, 13, 10, 13, 13, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 13, 13, 10, 13, 13, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340899825 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825 Building ZINC001340899825 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340899825 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 761) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: O=C(N1NC(=O)C[C@]12CCNC2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001340899825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340899825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001340899825 none O=C(N1NC(=O)C[C@]12CCNC2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 15, 15, 10, 15, 15, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 762) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: O=C(N1NC(=O)C[C@]12CCNC2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001340899825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340899825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001340899825 none O=C(N1NC(=O)C[C@]12CCNC2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 10, 10, 10, 10, 13, 13, 10, 13, 13, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 13, 13, 10, 13, 13, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340899825 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899825 Building ZINC001340899827 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340899827 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/763 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1NC(=O)C[C@@]12CCNC2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001340899827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340899827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001340899827 none O=C(N1NC(=O)C[C@@]12CCNC2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 13, 13, 10, 13, 13, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 13, 13, 10, 13, 13, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/764 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/764' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1NC(=O)C[C@@]12CCNC2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001340899827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340899827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001340899827 none O=C(N1NC(=O)C[C@@]12CCNC2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 10, 10, 10, 10, 16, 16, 10, 16, 16, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 16, 16, 10, 16, 16, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340899827 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827 Building ZINC001340899827 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340899827 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 763) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: O=C(N1NC(=O)C[C@@]12CCNC2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001340899827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340899827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001340899827 none O=C(N1NC(=O)C[C@@]12CCNC2)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 13, 13, 10, 13, 13, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 13, 13, 10, 13, 13, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 764) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: O=C(N1NC(=O)C[C@@]12CCNC2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001340899827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340899827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001340899827 none O=C(N1NC(=O)C[C@@]12CCNC2)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 10, 10, 10, 10, 16, 16, 10, 16, 16, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 16, 16, 10, 16, 16, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340899827 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340899827 Building ZINC001340928440 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340928440 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/765 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001340928440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340928440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340928440 none COC(=O)NCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 23, 8, 7, 8, 7, 7, 7, 7, 7, 7, 6, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 40, 23, 23, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/766 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001340928440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340928440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340928440 none COC(=O)NCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 10, 7, 10, 7, 7, 7, 7, 7, 7, 4, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 39, 21, 21, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340928440 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440 Building ZINC001340928440 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340928440 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 765) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)NCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001340928440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340928440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340928440 none COC(=O)NCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 23, 8, 7, 8, 7, 7, 7, 7, 7, 7, 6, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 40, 23, 23, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 766) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)NCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001340928440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340928440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340928440 none COC(=O)NCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 10, 7, 10, 7, 7, 7, 7, 7, 7, 4, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 39, 21, 21, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340928440 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340928440 Building ZINC001340959110 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340959110 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/767 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COCC(F)F)C[C@H]21) `ZINC001340959110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340959110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340959110 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COCC(F)F)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 8, 8, 23, 41, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 23, 23, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/768 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/768' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COCC(F)F)C[C@H]21) `ZINC001340959110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340959110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340959110 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COCC(F)F)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 8, 8, 24, 39, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 24, 24, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340959110 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110 Building ZINC001340959110 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340959110 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 767) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COCC(F)F)C[C@H]21) `ZINC001340959110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340959110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340959110 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COCC(F)F)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 8, 8, 23, 41, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 23, 23, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 768) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COCC(F)F)C[C@H]21) `ZINC001340959110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340959110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001340959110 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COCC(F)F)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 8, 8, 24, 39, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 24, 24, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340959110 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340959110 Building ZINC001340960448 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340960448 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/769 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001340960448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340960448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340960448 none COCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 38, 23, 10, 7, 10, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 46, 46, 23, 23, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/770 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/770' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001340960448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340960448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340960448 none COCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 36, 23, 9, 6, 9, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 44, 44, 23, 23, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340960448 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448 Building ZINC001340960448 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340960448 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 769) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001340960448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340960448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340960448 none COCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 38, 23, 10, 7, 10, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 46, 46, 23, 23, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 770) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001340960448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340960448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340960448 none COCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 36, 23, 9, 6, 9, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 44, 44, 23, 23, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340960448 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960448 Building ZINC001340960489 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340960489 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/771 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001340960489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340960489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340960489 none COC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 50, 22, 10, 6, 10, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 31, 22, 22, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/772 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001340960489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340960489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340960489 none COC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 19, 8, 4, 8, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 37, 19, 19, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340960489 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489 Building ZINC001340960489 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340960489 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 771) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001340960489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340960489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340960489 none COC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 50, 22, 10, 6, 10, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 31, 22, 22, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 772) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001340960489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340960489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340960489 none COC(=O)NCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 19, 8, 4, 8, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 37, 19, 19, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340960489 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340960489 Building ZINC001340962712 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340962712 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/773 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001340962712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340962712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340962712 none CCNC(=O)CC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 24, 32, 6, 4, 6, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 32, 24, 24, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/774 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/774' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001340962712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340962712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340962712 none CCNC(=O)CC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need 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, 23, 32, 6, 4, 6, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 32, 23, 23, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340962712 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712 Building ZINC001340962712 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001340962712 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 773) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCNC(=O)CC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001340962712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001340962712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340962712 none CCNC(=O)CC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 24, 32, 6, 4, 6, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 32, 24, 24, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 774) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCNC(=O)CC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001340962712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001340962712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001340962712 none CCNC(=O)CC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need 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, 23, 32, 6, 4, 6, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 32, 23, 23, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001340962712 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001340962712 Building ZINC001341024281 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341024281 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/775 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]12C[C@H](N)C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)C2) `ZINC001341024281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341024281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001341024281 none COC(=O)[C@]12C[C@H](N)C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 50, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 1, 10, 1, 1, 1, 2, 2, 1, 1, 2, 2, 25, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 25, 25] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/776 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]12C[C@H](N)C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)C2) `ZINC001341024281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341024281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001341024281 none COC(=O)[C@]12C[C@H](N)C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 50, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 1, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 25, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 25, 25] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341024281 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281 Building ZINC001341024281 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341024281 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 775) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@]12C[C@H](N)C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)C2) `ZINC001341024281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341024281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001341024281 none COC(=O)[C@]12C[C@H](N)C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 50, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 1, 10, 1, 1, 1, 2, 2, 1, 1, 2, 2, 25, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 25, 25] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 776) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC(=O)[C@]12C[C@H](N)C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)C2) `ZINC001341024281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341024281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001341024281 none COC(=O)[C@]12C[C@H](N)C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 50, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 1, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 25, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 25, 25] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341024281 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341024281 Building ZINC001341046679 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341046679 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/777 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2NC(=O)CC23CCNCC3)cn1) `ZINC001341046679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341046679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001341046679 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2NC(=O)CC23CCNCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 3, 8, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/778 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2NC(=O)CC23CCNCC3)cn1) `ZINC001341046679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341046679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001341046679 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2NC(=O)CC23CCNCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 16, 7, 7, 1, 1, 1, 3, 11, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341046679 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679 Building ZINC001341046679 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341046679 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 777) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2NC(=O)CC23CCNCC3)cn1) `ZINC001341046679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341046679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001341046679 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2NC(=O)CC23CCNCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 3, 8, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 778) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2NC(=O)CC23CCNCC3)cn1) `ZINC001341046679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341046679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001341046679 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2NC(=O)CC23CCNCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 16, 7, 7, 1, 1, 1, 3, 11, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341046679 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341046679 Building ZINC001341117445 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341117445 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/779 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001341117445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341117445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341117445 none C[C@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 31, 31, 44, 50, 50, 8, 17, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 31, 31, 31, 44, 44, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/780 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001341117445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341117445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341117445 none C[C@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 29, 29, 41, 50, 50, 8, 17, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 29, 29, 29, 41, 41, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341117445 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445 Building ZINC001341117445 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341117445 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 779) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001341117445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341117445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341117445 none C[C@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 31, 31, 44, 50, 50, 8, 17, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 31, 31, 31, 44, 44, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 780) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001341117445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341117445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341117445 none C[C@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 29, 29, 41, 50, 50, 8, 17, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 29, 29, 29, 41, 41, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341117445 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117445 Building ZINC001341117446 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341117446 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/781 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001341117446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341117446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341117446 none C[C@@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 32, 32, 46, 50, 50, 7, 16, 7, 7, 7, 7, 7, 7, 3, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 32, 32, 32, 46, 46, 50, 50, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/782 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001341117446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341117446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341117446 none C[C@@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 30, 30, 45, 50, 50, 8, 16, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 30, 30, 30, 45, 45, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341117446 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446 Building ZINC001341117446 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341117446 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 781) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001341117446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341117446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341117446 none C[C@@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 32, 32, 46, 50, 50, 7, 16, 7, 7, 7, 7, 7, 7, 3, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 32, 32, 32, 46, 46, 50, 50, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 782) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001341117446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341117446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341117446 none C[C@@H](CC(N)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 30, 30, 45, 50, 50, 8, 16, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 30, 30, 30, 45, 45, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341117446 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341117446 Building ZINC001341123712 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341123712 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/783 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(=O)NC3CC3)CC2)c1) `ZINC001341123712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341123712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001341123712 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(=O)NC3CC3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 7, 9, 9, 9, 9, 12, 12, 19, 19, 19, 31, 31, 9, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 19, 31, 31, 31, 31, 31, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/784 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(=O)NC3CC3)CC2)c1) `ZINC001341123712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341123712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001341123712 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(=O)NC3CC3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 7, 9, 9, 9, 9, 10, 10, 15, 15, 15, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 15, 27, 27, 27, 27, 27, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341123712 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712 Building ZINC001341123712 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341123712 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 783) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(=O)NC3CC3)CC2)c1) `ZINC001341123712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341123712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001341123712 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(=O)NC3CC3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 7, 9, 9, 9, 9, 12, 12, 19, 19, 19, 31, 31, 9, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 19, 31, 31, 31, 31, 31, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 784) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(=O)NC3CC3)CC2)c1) `ZINC001341123712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341123712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001341123712 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(=O)NC3CC3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 7, 9, 9, 9, 9, 10, 10, 15, 15, 15, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 15, 27, 27, 27, 27, 27, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341123712 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341123712 Building ZINC001341251537 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341251537 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/785 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CC[C@@H](C2)N3C2CCNCC2)cn1) `ZINC001341251537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341251537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341251537 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CC[C@@H](C2)N3C2CCNCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 53 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/786 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/786' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CC[C@@H](C2)N3C2CCNCC2)cn1) `ZINC001341251537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341251537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341251537 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CC[C@@H](C2)N3C2CCNCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 26, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 59 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341251537 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537 Building ZINC001341251537 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341251537 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 785) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CC[C@@H](C2)N3C2CCNCC2)cn1) `ZINC001341251537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341251537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341251537 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CC[C@@H](C2)N3C2CCNCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 53 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 786) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CC[C@@H](C2)N3C2CCNCC2)cn1) `ZINC001341251537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341251537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341251537 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CC[C@@H](C2)N3C2CCNCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 26, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 59 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341251537 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341251537 Building ZINC001341314110 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314110 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/787 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341314110 none CC[C@@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 14, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 33, 19, 33, 33, 49, 8, 19, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 38, 38, 38, 38, 38, 49, 49, 49, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/788 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/788' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341314110 none CC[C@@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 14, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 36, 22, 36, 36, 50, 10, 22, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 44, 44, 44, 44, 44, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 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: 242 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314110 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110 Building ZINC001341314110 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314110 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 787) grep: /scratch/xiaobo/2379/xbv-8058097.48/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@@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341314110 none CC[C@@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 14, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 33, 19, 33, 33, 49, 8, 19, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 38, 38, 38, 38, 38, 49, 49, 49, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 788) grep: /scratch/xiaobo/2379/xbv-8058097.48/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@@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341314110 none CC[C@@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 14, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 36, 22, 36, 36, 50, 10, 22, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 44, 44, 44, 44, 44, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 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: 242 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314110 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314110 Building ZINC001341314112 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314112 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/789 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341314112 none CC[C@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 14, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 39, 23, 39, 39, 50, 10, 23, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 45, 45, 45, 45, 45, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 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/2379/xbv-8058097.48/working/building/ZINC001341314112 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/790 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/790' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341314112 none CC[C@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 14, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 36, 21, 36, 36, 50, 12, 21, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 41, 41, 41, 41, 41, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 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: 230 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314112 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112 Building ZINC001341314112 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314112 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 789) grep: /scratch/xiaobo/2379/xbv-8058097.48/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@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341314112 none CC[C@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 14, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 39, 23, 39, 39, 50, 10, 23, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 45, 45, 45, 45, 45, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 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/2379/xbv-8058097.48/working/building/ZINC001341314112 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 790) grep: /scratch/xiaobo/2379/xbv-8058097.48/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@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001341314112 none CC[C@H](SC)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 14, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 36, 21, 36, 36, 50, 12, 21, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 41, 41, 41, 41, 41, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 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: 230 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314112 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314112 Building ZINC001341314205 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314205 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/791 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCOC2)C[C@H]1O) `ZINC001341314205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314205 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 11, 11, 40, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/792 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/792' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCOC2)C[C@H]1O) `ZINC001341314205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314205 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 11, 11, 38, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 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: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314205 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205 Building ZINC001341314205 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314205 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 791) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCOC2)C[C@H]1O) `ZINC001341314205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314205 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 11, 11, 40, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 792) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCOC2)C[C@H]1O) `ZINC001341314205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314205 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 11, 11, 38, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 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: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314205 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314205 Building ZINC001341314207 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314207 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/793 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCOC2)C[C@H]1O) `ZINC001341314207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314207 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 14, 14, 40, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/794 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/794' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCOC2)C[C@H]1O) `ZINC001341314207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314207 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 13, 13, 38, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314207 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207 Building ZINC001341314207 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314207 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 793) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCOC2)C[C@H]1O) `ZINC001341314207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314207 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 14, 14, 40, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 794) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCOC2)C[C@H]1O) `ZINC001341314207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314207 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 13, 13, 38, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314207 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314207 Building ZINC001341314529 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314529 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/795 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341314529 none COCCC[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 36, 24, 13, 24, 24, 7, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 37, 37, 36, 36, 24, 24, 24, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/796 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/796' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341314529 none COCCC[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 32, 23, 12, 23, 23, 7, 12, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 32, 32, 32, 32, 23, 23, 23, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 258 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314529 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529 Building ZINC001341314529 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314529 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 795) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCC[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341314529 none COCCC[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 36, 24, 13, 24, 24, 7, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 37, 37, 36, 36, 24, 24, 24, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 796) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCC[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341314529 none COCCC[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 32, 23, 12, 23, 23, 7, 12, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 32, 32, 32, 32, 23, 23, 23, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 258 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314529 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314529 Building ZINC001341314530 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314530 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/797 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341314530 none COCCC[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 29, 29, 20, 10, 20, 20, 6, 10, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 29, 29, 29, 29, 20, 20, 20, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/798 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/798' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341314530 none COCCC[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 26, 13, 26, 26, 9, 13, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 34, 34, 34, 34, 26, 26, 26, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314530 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530 Building ZINC001341314530 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314530 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 797) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCC[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341314530 none COCCC[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 29, 29, 20, 10, 20, 20, 6, 10, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 29, 29, 29, 29, 20, 20, 20, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 798) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCC[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341314530 none COCCC[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 26, 13, 26, 26, 9, 13, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 34, 34, 34, 34, 26, 26, 26, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314530 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314530 Building ZINC001341314531 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314531 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/799 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2)C[C@H]1O) `ZINC001341314531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341314531 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 23, 23, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/800 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2)C[C@H]1O) `ZINC001341314531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341314531 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 23, 23, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314531 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531 Building ZINC001341314531 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314531 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 799) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2)C[C@H]1O) `ZINC001341314531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341314531 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 23, 23, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 800) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2)C[C@H]1O) `ZINC001341314531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341314531 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 23, 23, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314531 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314531 Building ZINC001341314642 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314642 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/801 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccncc2)C[C@H]1O) `ZINC001341314642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341314642 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccncc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 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, 2, 2, 3, 12, 12, 12, 12, 29, 29, 48, 49, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 48, 48, 49, 49, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/802 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/802' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccncc2)C[C@H]1O) `ZINC001341314642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341314642 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccncc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 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, 2, 2, 4, 11, 11, 11, 11, 28, 28, 49, 49, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 49, 49, 49, 49, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314642 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642 Building ZINC001341314642 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314642 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 801) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccncc2)C[C@H]1O) `ZINC001341314642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341314642 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccncc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 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, 2, 2, 3, 12, 12, 12, 12, 29, 29, 48, 49, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 48, 48, 49, 49, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 802) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccncc2)C[C@H]1O) `ZINC001341314642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341314642 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccncc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 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, 2, 2, 4, 11, 11, 11, 11, 28, 28, 49, 49, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 49, 49, 49, 49, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314642 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314642 Building ZINC001341314745 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314745 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/803 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001341314745 none CCc1cnccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 40, 40, 24, 40, 40, 21, 9, 21, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 40, 40, 40, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/804 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/804' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001341314745 none CCc1cnccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 40, 40, 35, 40, 40, 20, 11, 20, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 40, 40, 40, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314745 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745 Building ZINC001341314745 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314745 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 803) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1cnccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001341314745 none CCc1cnccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 40, 40, 24, 40, 40, 21, 9, 21, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 40, 40, 40, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 804) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1cnccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001341314745 none CCc1cnccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 40, 40, 35, 40, 40, 20, 11, 20, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 40, 40, 40, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314745 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314745 Building ZINC001341314835 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314835 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/805 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)[nH]2)C[C@H]1O) `ZINC001341314835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001341314835 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)[nH]2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 6, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 31, 31, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/806 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/806' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)[nH]2)C[C@H]1O) `ZINC001341314835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001341314835 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)[nH]2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 6, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314835 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835 Building ZINC001341314835 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314835 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 805) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)[nH]2)C[C@H]1O) `ZINC001341314835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001341314835 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)[nH]2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 6, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 31, 31, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 806) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)[nH]2)C[C@H]1O) `ZINC001341314835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001341314835 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)[nH]2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 6, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314835 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314835 Building ZINC001341314902 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314902 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/807 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccccc2O)C[C@H]1O) `ZINC001341314902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341314902 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccccc2O)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 26, 26, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 50, 100, 15, 15, 45] 300 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 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: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/808 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccccc2O)C[C@H]1O) `ZINC001341314902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341314902 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccccc2O)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 27, 27, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 100, 12, 12, 36] 300 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 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: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314902 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902 Building ZINC001341314902 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314902 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 807) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccccc2O)C[C@H]1O) `ZINC001341314902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341314902 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccccc2O)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 26, 26, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 50, 100, 15, 15, 45] 300 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 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: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 808) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccccc2O)C[C@H]1O) `ZINC001341314902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341314902 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccccc2O)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 27, 27, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 100, 12, 12, 36] 300 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 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: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341314902 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341314902 Building ZINC001341315189 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315189 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/809 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(F)cn2)C[C@H]1O) `ZINC001341315189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315189 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(F)cn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 31, 31, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 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: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/810 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(F)cn2)C[C@H]1O) `ZINC001341315189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315189 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(F)cn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 30, 30, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 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: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315189 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189 Building ZINC001341315189 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315189 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 809) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(F)cn2)C[C@H]1O) `ZINC001341315189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315189 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(F)cn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 31, 31, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 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: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 810) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(F)cn2)C[C@H]1O) `ZINC001341315189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315189 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(F)cn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 30, 30, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 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: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315189 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315189 Building ZINC001341315293 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315293 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/811 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341315293 none Cc1noc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 7, 25, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 133 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/812 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341315293 none Cc1noc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 8, 26, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 141 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315293 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293 Building ZINC001341315293 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315293 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 811) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1noc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341315293 none Cc1noc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 7, 25, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 133 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 812) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1noc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341315293 none Cc1noc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 8, 26, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 141 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315293 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315293 Building ZINC001341315315 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315315 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/813 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001341315315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341315315 none CCOCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 24, 24, 8, 24, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 24, 24, 50, 50, 50, 50, 50, 49, 49, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 24, 24, 24] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/814 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001341315315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341315315 none CCOCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 26, 26, 8, 26, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 26, 26, 50, 50, 50, 50, 50, 49, 49, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315315 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315 Building ZINC001341315315 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315315 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 813) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCOCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001341315315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341315315 none CCOCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 24, 24, 8, 24, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 24, 24, 50, 50, 50, 50, 50, 49, 49, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 24, 24, 24] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 814) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCOCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001341315315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341315315 none CCOCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 26, 26, 8, 26, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 26, 26, 50, 50, 50, 50, 50, 49, 49, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315315 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315315 Building ZINC001341315318 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315318 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/815 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1) `ZINC001341315318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341315318 none Cc1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 27, 11, 27, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 100] 300 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: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/816 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1) `ZINC001341315318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341315318 none Cc1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 30, 12, 30, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 100] 300 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: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315318 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318 Building ZINC001341315318 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315318 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 815) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1) `ZINC001341315318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341315318 none Cc1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 27, 11, 27, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 100] 300 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: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 816) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1) `ZINC001341315318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341315318 none Cc1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 30, 12, 30, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 100] 300 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: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315318 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315318 Building ZINC001341315362 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315362 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/817 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3CCCC[C@@H]32)C[C@H]1O) `ZINC001341315362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341315362 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3CCCC[C@@H]32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/818 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3CCCC[C@@H]32)C[C@H]1O) `ZINC001341315362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341315362 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3CCCC[C@@H]32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/2379/xbv-8058097.48/working/building/ZINC001341315362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315362 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362 Building ZINC001341315362 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315362 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 817) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3CCCC[C@@H]32)C[C@H]1O) `ZINC001341315362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341315362 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3CCCC[C@@H]32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 818) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3CCCC[C@@H]32)C[C@H]1O) `ZINC001341315362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341315362 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3CCCC[C@@H]32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/2379/xbv-8058097.48/working/building/ZINC001341315362 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315362 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315362 Building ZINC001341315373 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315373 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/819 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)/C=C/c2ccc[nH]2)C[C@H]1O) `ZINC001341315373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315373 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)/C=C/c2ccc[nH]2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 14, 14, 31, 31, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 31, 31, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/820 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)/C=C/c2ccc[nH]2)C[C@H]1O) `ZINC001341315373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315373 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)/C=C/c2ccc[nH]2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 17, 17, 38, 38, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 38, 38, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315373 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373 Building ZINC001341315373 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315373 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 819) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)/C=C/c2ccc[nH]2)C[C@H]1O) `ZINC001341315373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315373 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)/C=C/c2ccc[nH]2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 14, 14, 31, 31, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 31, 31, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 820) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)/C=C/c2ccc[nH]2)C[C@H]1O) `ZINC001341315373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315373 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)/C=C/c2ccc[nH]2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 17, 17, 38, 38, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 38, 38, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315373 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315373 Building ZINC001341315988 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315988 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/821 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001341315988 none CC(C)C[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 30, 44, 44, 11, 30, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 238 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/822 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001341315988 none CC(C)C[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 45, 32, 45, 45, 12, 32, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 45, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 233 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315988 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988 Building ZINC001341315988 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315988 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 821) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001341315988 none CC(C)C[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 30, 44, 44, 11, 30, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 238 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 822) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001341315988 none CC(C)C[C@@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 45, 32, 45, 45, 12, 32, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 45, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 233 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315988 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315988 Building ZINC001341315992 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315992 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/823 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001341315992 none CC(C)C[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 40, 50, 50, 12, 40, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 203 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/824 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001341315992 none CC(C)C[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 44, 50, 50, 15, 44, 15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 202 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315992 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992 Building ZINC001341315992 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315992 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 823) grep: /scratch/xiaobo/2379/xbv-8058097.48/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@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001341315992 none CC(C)C[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 40, 50, 50, 12, 40, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 203 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 824) grep: /scratch/xiaobo/2379/xbv-8058097.48/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@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001341315992 none CC(C)C[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 44, 50, 50, 15, 44, 15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 202 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341315992 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341315992 Building ZINC001341316397 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316397 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/825 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001341316397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001341316397 none CCc1cncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 25, 25, 25, 25, 25, 14, 7, 14, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 25, 50, 50, 50, 50, 50, 25, 25, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25] 150 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]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/826 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/826' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001341316397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001341316397 none CCc1cncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 26, 26, 26, 26, 26, 15, 7, 15, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 26, 50, 50, 50, 50, 50, 26, 26, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26] 150 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]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341316397 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397 Building ZINC001341316397 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316397 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 825) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1cncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001341316397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001341316397 none CCc1cncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 25, 25, 25, 25, 25, 14, 7, 14, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 25, 50, 50, 50, 50, 50, 25, 25, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25] 150 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]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 826) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1cncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001341316397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001341316397 none CCc1cncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 26, 26, 26, 26, 26, 15, 7, 15, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 26, 50, 50, 50, 50, 50, 26, 26, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26] 150 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]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341316397 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316397 Building ZINC001341316797 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316797 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/827 `/scratch/xiaobo/2379/xbv-8058097.48/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)N[C@@H]1CN(C(=O)[C@]2(C)C[C@H]3C[C@H]3C2)C[C@H]1O) `ZINC001341316797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341316797 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)C[C@H]3C[C@H]3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 38, 43, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/828 `/scratch/xiaobo/2379/xbv-8058097.48/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)N[C@@H]1CN(C(=O)[C@]2(C)C[C@H]3C[C@H]3C2)C[C@H]1O) `ZINC001341316797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341316797 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)C[C@H]3C[C@H]3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 6, 14, 14, 14, 14, 39, 44, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 135 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341316797 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797 Building ZINC001341316797 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316797 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 827) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)N[C@@H]1CN(C(=O)[C@]2(C)C[C@H]3C[C@H]3C2)C[C@H]1O) `ZINC001341316797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341316797 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)C[C@H]3C[C@H]3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 38, 43, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 828) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)N[C@@H]1CN(C(=O)[C@]2(C)C[C@H]3C[C@H]3C2)C[C@H]1O) `ZINC001341316797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341316797 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)C[C@H]3C[C@H]3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 6, 14, 14, 14, 14, 39, 44, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 135 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341316797 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341316797 Building ZINC001341317032 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341317032 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/829 `/scratch/xiaobo/2379/xbv-8058097.48/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)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2C2CCC2)C[C@H]1O) `ZINC001341317032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341317032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341317032 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2C2CCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 18, 18, 40, 40, 40, 40, 40, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 40, 40, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/830 `/scratch/xiaobo/2379/xbv-8058097.48/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)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2C2CCC2)C[C@H]1O) `ZINC001341317032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341317032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341317032 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2C2CCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 19, 19, 40, 40, 40, 40, 42, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 40, 40, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341317032 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032 Building ZINC001341317032 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341317032 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 829) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2C2CCC2)C[C@H]1O) `ZINC001341317032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341317032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341317032 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2C2CCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 18, 18, 40, 40, 40, 40, 40, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 40, 40, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 830) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2C2CCC2)C[C@H]1O) `ZINC001341317032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341317032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341317032 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@H]2C2CCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 19, 19, 40, 40, 40, 40, 42, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 40, 40, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341317032 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317032 Building ZINC001341317092 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341317092 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/831 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2sccc2F)C[C@H]1O) `ZINC001341317092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341317092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001341317092 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2sccc2F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 14, 1, 1, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 22, 22, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/832 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2sccc2F)C[C@H]1O) `ZINC001341317092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341317092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001341317092 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2sccc2F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 14, 1, 1, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 21, 21, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 11, 11, 33] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341317092 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092 Building ZINC001341317092 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341317092 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 831) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2sccc2F)C[C@H]1O) `ZINC001341317092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341317092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001341317092 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2sccc2F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 14, 1, 1, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 22, 22, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 832) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2sccc2F)C[C@H]1O) `ZINC001341317092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341317092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001341317092 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2sccc2F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 14, 1, 1, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 21, 21, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 11, 11, 33] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341317092 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341317092 Building ZINC001341318263 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318263 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/833 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001341318263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341318263 none COCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 36, 34, 11, 34, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 36, 36, 36, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 36, 36, 36, 36, 36, 36] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/834 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/834' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001341318263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341318263 none COCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 31, 12, 31, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 35, 35, 35, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 35, 35, 35, 35] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 229 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341318263 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263 Building ZINC001341318263 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318263 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 833) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001341318263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341318263 none COCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 36, 34, 11, 34, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 36, 36, 36, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 36, 36, 36, 36, 36, 36] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 834) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001341318263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341318263 none COCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 31, 12, 31, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 35, 35, 35, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 35, 35, 35, 35] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 229 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341318263 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318263 Building ZINC001341318283 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318283 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/835 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001341318283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341318283 none CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need 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, 19, 8, 19, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 40, 40, 50, 50, 50, 50, 50, 40, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/836 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/836' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001341318283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341318283 none CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 41, 41, 23, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 41, 41, 50, 50, 50, 50, 50, 41, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341318283 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283 Building ZINC001341318283 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318283 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 835) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001341318283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341318283 none CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need 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, 19, 8, 19, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 40, 40, 50, 50, 50, 50, 50, 40, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 836) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001341318283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341318283 none CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 41, 41, 23, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 41, 41, 50, 50, 50, 50, 50, 41, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341318283 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341318283 Building ZINC001341327228 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341327228 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/837 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC(F)(F)F)C1) `ZINC001341327228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341327228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341327228 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC(F)(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', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 4, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 45, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 16, 45, 45, 50, 50, 5, 5] 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: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/838 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC(F)(F)F)C1) `ZINC001341327228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341327228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341327228 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC(F)(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', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 43, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 17, 43, 43, 50, 50, 8, 8] 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: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341327228 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228 Building ZINC001341327228 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341327228 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 837) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC(F)(F)F)C1) `ZINC001341327228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341327228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341327228 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC(F)(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', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 4, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 45, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 16, 45, 45, 50, 50, 5, 5] 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: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 838) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC(F)(F)F)C1) `ZINC001341327228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341327228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341327228 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC(F)(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', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 43, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 17, 43, 43, 50, 50, 8, 8] 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: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341327228 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341327228 Building ZINC001341473704 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341473704 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/839 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2cccc2)C1) `ZINC001341473704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341473704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341473704 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2cccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 4, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 42, 35, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 10, 42, 42, 47, 47, 47, 49, 50, 50, 50, 50, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/840 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/840' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2cccc2)C1) `ZINC001341473704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341473704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341473704 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2cccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 43, 37, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 10, 43, 43, 49, 49, 50, 49, 50, 50, 50, 50, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341473704 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704 Building ZINC001341473704 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341473704 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 839) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2cccc2)C1) `ZINC001341473704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341473704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341473704 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2cccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 4, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 42, 35, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 10, 42, 42, 47, 47, 47, 49, 50, 50, 50, 50, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 840) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2cccc2)C1) `ZINC001341473704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341473704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341473704 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2cccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 43, 37, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 10, 43, 43, 49, 49, 50, 49, 50, 50, 50, 50, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341473704 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341473704 Building ZINC001341492808 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341492808 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/841 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001341492808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341492808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341492808 none CNC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 27, 13, 8, 13, 13, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 34, 34, 34, 34, 27, 27, 39, 8, 8, 4, 4, 4, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 202 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/842 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/842' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001341492808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341492808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341492808 none CNC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 26, 16, 9, 16, 16, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 33, 33, 33, 33, 26, 26, 48, 9, 9, 4, 4, 4, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 210 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341492808 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808 Building ZINC001341492808 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341492808 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 841) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001341492808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341492808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341492808 none CNC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 27, 13, 8, 13, 13, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 34, 34, 34, 34, 27, 27, 39, 8, 8, 4, 4, 4, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 202 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 842) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001341492808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341492808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341492808 none CNC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 26, 16, 9, 16, 16, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 33, 33, 33, 33, 26, 26, 48, 9, 9, 4, 4, 4, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 210 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341492808 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492808 Building ZINC001341492809 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341492809 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/843 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001341492809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341492809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341492809 none CNC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 32, 18, 10, 18, 18, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 36, 36, 36, 36, 32, 32, 54, 10, 10, 4, 4, 4, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/844 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001341492809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341492809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341492809 none CNC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 29, 18, 8, 18, 18, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 34, 34, 34, 34, 29, 29, 54, 8, 8, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341492809 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809 Building ZINC001341492809 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341492809 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 843) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001341492809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341492809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341492809 none CNC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 32, 18, 10, 18, 18, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 36, 36, 36, 36, 32, 32, 54, 10, 10, 4, 4, 4, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 844) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CNC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001341492809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341492809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341492809 none CNC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 29, 18, 8, 18, 18, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 34, 34, 34, 34, 29, 29, 54, 8, 8, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341492809 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341492809 Building ZINC001341518895 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341518895 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/845 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001341518895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341518895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001341518895 none COC[C@@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 15, 15, 6, 15, 15, 6, 28, 28, 28, 25, 25, 10, 10, 10, 10, 10, 10, 10, 6, 15, 15, 6, 15, 15, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/846 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/846' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001341518895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341518895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001341518895 none COC[C@@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 28, 28, 28, 22, 22, 10, 10, 10, 10, 10, 10, 10, 6, 13, 13, 6, 13, 13, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341518895 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895 Building ZINC001341518895 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341518895 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 845) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001341518895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341518895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001341518895 none COC[C@@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 15, 15, 6, 15, 15, 6, 28, 28, 28, 25, 25, 10, 10, 10, 10, 10, 10, 10, 6, 15, 15, 6, 15, 15, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 846) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001341518895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341518895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001341518895 none COC[C@@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 28, 28, 28, 22, 22, 10, 10, 10, 10, 10, 10, 10, 6, 13, 13, 6, 13, 13, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341518895 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518895 Building ZINC001341518897 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341518897 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/847 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001341518897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341518897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001341518897 none COC[C@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 12, 12, 12, 12, 12, 12, 12, 10, 3, 10, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 31, 31, 31, 24, 24, 12, 12, 12, 12, 12, 12, 12, 6, 14, 14, 6, 14, 14, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/848 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001341518897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341518897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001341518897 none COC[C@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 10, 10, 10, 10, 10, 10, 9, 3, 9, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 29, 29, 29, 25, 25, 10, 10, 10, 10, 10, 10, 10, 6, 12, 12, 6, 12, 12, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341518897 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897 Building ZINC001341518897 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341518897 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 847) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC[C@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001341518897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341518897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001341518897 none COC[C@H]1CNCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 12, 12, 12, 12, 12, 12, 12, 10, 3, 10, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 31, 31, 31, 24, 24, 12, 12, 12, 12, 12, 12, 12, 6, 14, 14, 6, 14, 14, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 848) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC[C@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001341518897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341518897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001341518897 none COC[C@H]1CNCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 10, 10, 10, 10, 10, 10, 9, 3, 9, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 29, 29, 29, 25, 25, 10, 10, 10, 10, 10, 10, 10, 6, 12, 12, 6, 12, 12, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341518897 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341518897 Building ZINC001341615946 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341615946 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/849 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCC1) `ZINC001341615946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341615946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341615946 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 45, 21, 17, 17, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 45, 45, 45, 50, 50, 50, 50, 50, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 45, 45, 45, 45, 45, 45] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/850 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCC1) `ZINC001341615946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341615946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341615946 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 46, 26, 24, 24, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 46, 46, 46, 50, 50, 50, 50, 50, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341615946 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946 Building ZINC001341615946 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341615946 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 849) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCC1) `ZINC001341615946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341615946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341615946 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 45, 21, 17, 17, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 45, 45, 45, 50, 50, 50, 50, 50, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 45, 45, 45, 45, 45, 45] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 850) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCC1) `ZINC001341615946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341615946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341615946 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 46, 26, 24, 24, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 46, 46, 46, 50, 50, 50, 50, 50, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341615946 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341615946 Building ZINC001341706355 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341706355 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/851 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341706355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341706355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341706355 none CCC[C@@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 47, 30, 11, 30, 30, 32, 32, 11, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/852 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341706355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341706355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341706355 none CCC[C@@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 31, 14, 31, 31, 32, 32, 14, 14, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341706355 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355 Building ZINC001341706355 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341706355 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 851) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCC[C@@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341706355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341706355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341706355 none CCC[C@@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 47, 30, 11, 30, 30, 32, 32, 11, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 852) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCC[C@@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341706355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341706355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341706355 none CCC[C@@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 31, 14, 31, 31, 32, 32, 14, 14, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341706355 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706355 Building ZINC001341706356 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341706356 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/853 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341706356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341706356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341706356 none CCC[C@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need 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, 28, 10, 28, 28, 31, 31, 10, 10, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/854 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341706356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341706356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341706356 none CCC[C@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 11, 28, 28, 28, 28, 11, 11, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341706356 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356 Building ZINC001341706356 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341706356 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 853) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCC[C@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341706356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341706356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341706356 none CCC[C@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need 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, 28, 10, 28, 28, 31, 31, 10, 10, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 854) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCC[C@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341706356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341706356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001341706356 none CCC[C@H](OCC)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 11, 28, 28, 28, 28, 11, 11, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341706356 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341706356 Building ZINC001341708082 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341708082 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/855 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(OC3CNC3)CC2)cn1) `ZINC001341708082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341708082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001341708082 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(OC3CNC3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 6, 4, 4, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 20, 33, 33, 33, 6, 6, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/856 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(OC3CNC3)CC2)cn1) `ZINC001341708082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341708082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001341708082 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(OC3CNC3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 6, 6, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 22, 33, 33, 33, 8, 8, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341708082 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082 Building ZINC001341708082 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341708082 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 855) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(OC3CNC3)CC2)cn1) `ZINC001341708082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341708082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001341708082 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(OC3CNC3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 6, 4, 4, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 20, 33, 33, 33, 6, 6, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 856) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(OC3CNC3)CC2)cn1) `ZINC001341708082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341708082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001341708082 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(OC3CNC3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 6, 6, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 22, 33, 33, 33, 8, 8, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341708082 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341708082 Building ZINC001341752538 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341752538 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/857 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCNCC3=O)C2)c1) `ZINC001341752538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341752538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341752538 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCNCC3=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 10, 5, 1, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 2, 4, 4, 12, 12, 12, 12, 12, 18, 30, 30, 30, 30, 30, 30, 12, 6, 6, 6, 6, 2, 6, 6, 12, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 12, 12, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/858 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCNCC3=O)C2)c1) `ZINC001341752538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341752538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341752538 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCNCC3=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 10, 5, 1, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 2, 4, 4, 10, 10, 10, 10, 10, 13, 25, 25, 25, 25, 25, 25, 10, 4, 4, 4, 4, 2, 4, 4, 10, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 10, 10, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341752538 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538 Building ZINC001341752538 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341752538 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 857) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCNCC3=O)C2)c1) `ZINC001341752538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341752538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341752538 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCNCC3=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 10, 5, 1, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 2, 4, 4, 12, 12, 12, 12, 12, 18, 30, 30, 30, 30, 30, 30, 12, 6, 6, 6, 6, 2, 6, 6, 12, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 12, 12, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 858) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCNCC3=O)C2)c1) `ZINC001341752538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341752538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341752538 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](N3CCNCC3=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 10, 5, 1, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 2, 4, 4, 10, 10, 10, 10, 10, 13, 25, 25, 25, 25, 25, 25, 10, 4, 4, 4, 4, 2, 4, 4, 10, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 10, 10, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341752538 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752538 Building ZINC001341752544 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341752544 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/859 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCNCC3=O)C2)c1) `ZINC001341752544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341752544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341752544 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCNCC3=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 10, 5, 1, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 5, 1, 1, 1, 2, 3, 4, 8, 8, 8, 8, 8, 13, 28, 29, 29, 29, 29, 29, 8, 5, 5, 5, 5, 2, 5, 5, 8, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 8, 8, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/860 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/860' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCNCC3=O)C2)c1) `ZINC001341752544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341752544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341752544 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCNCC3=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 10, 5, 1, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 2, 5, 7, 11, 11, 11, 11, 11, 16, 25, 25, 25, 25, 25, 25, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 11, 11, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 63 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341752544 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544 Building ZINC001341752544 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341752544 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 859) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCNCC3=O)C2)c1) `ZINC001341752544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341752544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341752544 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCNCC3=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 10, 5, 1, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 5, 1, 1, 1, 2, 3, 4, 8, 8, 8, 8, 8, 13, 28, 29, 29, 29, 29, 29, 8, 5, 5, 5, 5, 2, 5, 5, 8, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 8, 8, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 860) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCNCC3=O)C2)c1) `ZINC001341752544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341752544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341752544 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](N3CCNCC3=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 10, 5, 1, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 2, 5, 7, 11, 11, 11, 11, 11, 16, 25, 25, 25, 25, 25, 25, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 11, 11, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 63 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341752544 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341752544 Building ZINC001341824702 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341824702 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/861 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)c1) `ZINC001341824702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341824702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001341824702 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 1, 5, 5, 3, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/862 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)c1) `ZINC001341824702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341824702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001341824702 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 1, 6, 6, 3, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341824702 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702 Building ZINC001341824702 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341824702 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 861) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)c1) `ZINC001341824702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341824702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001341824702 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 1, 5, 5, 3, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 862) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)c1) `ZINC001341824702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341824702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001341824702 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 1, 6, 6, 3, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341824702 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824702 Building ZINC001341824705 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341824705 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/863 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)c1) `ZINC001341824705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341824705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001341824705 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 1, 6, 6, 3, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/864 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/864' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)c1) `ZINC001341824705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341824705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001341824705 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 1, 5, 5, 3, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341824705 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705 Building ZINC001341824705 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341824705 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 863) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)c1) `ZINC001341824705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341824705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001341824705 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 1, 6, 6, 3, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 864) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)c1) `ZINC001341824705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341824705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001341824705 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 1, 5, 5, 3, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341824705 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341824705 Building ZINC001341952937 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341952937 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/865 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1) `ZINC001341952937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341952937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001341952937 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 13, 13, 5, 5, 1, 1, 1, 1, 5, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 23, 20, 23, 23, 23, 23, 22, 23, 23, 23, 23, 23, 23, 23, 23, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/866 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1) `ZINC001341952937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341952937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001341952937 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 5, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 24, 23, 24, 24, 24, 24, 23, 24, 24, 24, 24, 24, 24, 24, 24, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341952937 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937 Building ZINC001341952937 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341952937 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 865) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1) `ZINC001341952937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341952937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001341952937 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 13, 13, 5, 5, 1, 1, 1, 1, 5, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 23, 20, 23, 23, 23, 23, 22, 23, 23, 23, 23, 23, 23, 23, 23, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 866) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1) `ZINC001341952937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341952937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001341952937 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 5, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 24, 23, 24, 24, 24, 24, 23, 24, 24, 24, 24, 24, 24, 24, 24, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001341952937 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001341952937 Building ZINC001342064494 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342064494 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/867 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@H]2CCCC(=O)N2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342064494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342064494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064494 none C[C@@H]1CN(C(=O)[C@H]2CCCC(=O)N2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 30, 45, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/868 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@H]2CCCC(=O)N2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342064494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342064494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064494 none C[C@@H]1CN(C(=O)[C@H]2CCCC(=O)N2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 29, 43, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342064494 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494 Building ZINC001342064494 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342064494 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 867) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@H]2CCCC(=O)N2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342064494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342064494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064494 none C[C@@H]1CN(C(=O)[C@H]2CCCC(=O)N2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 30, 45, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 868) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@H]2CCCC(=O)N2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342064494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342064494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064494 none C[C@@H]1CN(C(=O)[C@H]2CCCC(=O)N2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 29, 43, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342064494 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064494 Building ZINC001342064712 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342064712 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/869 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342064712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342064712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064712 none C[C@@H]1CN(C(=O)[C@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 11, 11, 24, 35, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/870 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/870' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342064712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342064712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064712 none C[C@@H]1CN(C(=O)[C@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 13, 13, 23, 36, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342064712 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712 Building ZINC001342064712 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342064712 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 869) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1CN(C(=O)[C@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342064712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342064712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064712 none C[C@@H]1CN(C(=O)[C@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 11, 11, 24, 35, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 870) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1CN(C(=O)[C@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342064712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342064712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064712 none C[C@@H]1CN(C(=O)[C@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 13, 13, 23, 36, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342064712 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064712 Building ZINC001342064714 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342064714 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/871 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342064714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342064714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064714 none C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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: [12, 12, 12, 12, 12, 12, 27, 36, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/872 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342064714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342064714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064714 none C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 13, 13, 27, 34, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342064714 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714 Building ZINC001342064714 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342064714 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 871) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342064714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342064714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064714 none C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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: [12, 12, 12, 12, 12, 12, 27, 36, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 872) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342064714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342064714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064714 none C[C@@H]1CN(C(=O)[C@@H]2CCC(=O)NC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 13, 13, 27, 34, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342064714 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064714 Building ZINC001342064741 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342064741 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/873 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342064741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342064741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064741 none C[C@@H]1CN(C(=O)[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 35, 41, 50, 50, 50, 50, 50, 50, 50, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/874 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/874' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342064741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342064741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064741 none C[C@@H]1CN(C(=O)[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 29, 38, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342064741 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741 Building ZINC001342064741 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342064741 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 873) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1CN(C(=O)[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342064741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342064741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064741 none C[C@@H]1CN(C(=O)[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 35, 41, 50, 50, 50, 50, 50, 50, 50, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 874) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H]1CN(C(=O)[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342064741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342064741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342064741 none C[C@@H]1CN(C(=O)[C@H]2CCC(=O)N2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 29, 38, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342064741 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342064741 Building ZINC001342066785 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342066785 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/875 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001342066785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342066785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001342066785 none C[C@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 49, 18, 10, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 49, 50, 50, 50, 49, 49, 49, 44, 44, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/876 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/876' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001342066785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342066785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001342066785 none C[C@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 13, 19, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 43, 43, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 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]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342066785 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785 Building ZINC001342066785 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342066785 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 875) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001342066785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342066785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001342066785 none C[C@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 49, 18, 10, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 49, 50, 50, 50, 49, 49, 49, 44, 44, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 876) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001342066785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342066785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001342066785 none C[C@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 13, 19, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 43, 43, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 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]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342066785 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066785 Building ZINC001342066789 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342066789 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/877 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001342066789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342066789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001342066789 none C[C@@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 40, 49, 21, 12, 21, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 49, 50, 50, 50, 49, 49, 49, 40, 40, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 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]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/878 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001342066789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342066789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001342066789 none C[C@@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 12, 21, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 38, 38, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342066789 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789 Building ZINC001342066789 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342066789 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 877) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001342066789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342066789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001342066789 none C[C@@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 40, 49, 21, 12, 21, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 49, 50, 50, 50, 49, 49, 49, 40, 40, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 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]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 878) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001342066789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342066789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001342066789 none C[C@@H](CC(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 12, 21, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 38, 38, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342066789 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342066789 Building ZINC001342250268 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342250268 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/879 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](NCCO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001342250268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342250268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342250268 none O=C(N1CCC[C@H](NCCO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 11, 11, 11, 11, 11, 11, 18, 29, 34, 11, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 11, 11, 11, 11, 11, 11, 18, 29, 29, 34, 34, 102, 11, 11, 6, 8, 8, 6, 8, 8, 6] 150 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 238 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/880 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](NCCO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001342250268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342250268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342250268 none O=C(N1CCC[C@H](NCCO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 7, 10, 10, 10, 10, 10, 10, 19, 31, 35, 10, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 10, 10, 10, 10, 10, 10, 19, 31, 31, 35, 35, 105, 10, 10, 6, 9, 9, 6, 9, 9, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 254 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342250268 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268 Building ZINC001342250268 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342250268 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 879) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: O=C(N1CCC[C@H](NCCO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001342250268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342250268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342250268 none O=C(N1CCC[C@H](NCCO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 11, 11, 11, 11, 11, 11, 18, 29, 34, 11, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 11, 11, 11, 11, 11, 11, 18, 29, 29, 34, 34, 102, 11, 11, 6, 8, 8, 6, 8, 8, 6] 150 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 238 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 880) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: O=C(N1CCC[C@H](NCCO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001342250268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342250268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342250268 none O=C(N1CCC[C@H](NCCO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 7, 10, 10, 10, 10, 10, 10, 19, 31, 35, 10, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 10, 10, 10, 10, 10, 10, 19, 31, 31, 35, 35, 105, 10, 10, 6, 9, 9, 6, 9, 9, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 254 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342250268 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250268 Building ZINC001342250270 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342250270 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/881 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](NCCO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001342250270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342250270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342250270 none O=C(N1CCC[C@@H](NCCO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 6, 6, 6, 6, 6, 6, 15, 26, 32, 6, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 6, 6, 6, 6, 6, 6, 15, 26, 26, 32, 32, 96, 6, 6, 6, 10, 10, 8, 10, 10, 6] 150 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 256 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/882 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](NCCO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001342250270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342250270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342250270 none O=C(N1CCC[C@@H](NCCO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 15, 23, 28, 7, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 15, 23, 23, 28, 28, 84, 7, 7, 6, 7, 7, 7, 7, 7, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342250270 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270 Building ZINC001342250270 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342250270 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 881) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: O=C(N1CCC[C@@H](NCCO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001342250270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342250270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342250270 none O=C(N1CCC[C@@H](NCCO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 6, 6, 6, 6, 6, 6, 15, 26, 32, 6, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 6, 6, 6, 6, 6, 6, 15, 26, 26, 32, 32, 96, 6, 6, 6, 10, 10, 8, 10, 10, 6] 150 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 256 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 882) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: O=C(N1CCC[C@@H](NCCO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001342250270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342250270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342250270 none O=C(N1CCC[C@@H](NCCO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 15, 23, 28, 7, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 15, 23, 23, 28, 28, 84, 7, 7, 6, 7, 7, 7, 7, 7, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342250270 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342250270 Building ZINC001342440231 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342440231 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/883 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCNC[C@H]1CO) `ZINC001342440231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342440231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342440231 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCNC[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 17, 17, 7, 17, 17, 4, 4, 1, 1, 1, 2, 14, 14, 19, 19, 19, 19, 19, 19, 19, 37, 4, 4, 4, 17, 17, 6, 17, 17, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 37, 37, 111] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 274 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/884 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCNC[C@H]1CO) `ZINC001342440231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342440231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342440231 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCNC[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 16, 16, 16, 16, 16, 4, 4, 1, 1, 1, 2, 13, 13, 20, 20, 20, 20, 20, 20, 20, 37, 4, 4, 4, 16, 16, 16, 16, 16, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 37, 37, 111] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 253 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342440231 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231 Building ZINC001342440231 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342440231 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 883) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCNC[C@H]1CO) `ZINC001342440231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342440231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342440231 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCNC[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 17, 17, 7, 17, 17, 4, 4, 1, 1, 1, 2, 14, 14, 19, 19, 19, 19, 19, 19, 19, 37, 4, 4, 4, 17, 17, 6, 17, 17, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 37, 37, 111] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 274 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 884) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCNC[C@H]1CO) `ZINC001342440231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342440231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342440231 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCNC[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 16, 16, 16, 16, 16, 4, 4, 1, 1, 1, 2, 13, 13, 20, 20, 20, 20, 20, 20, 20, 37, 4, 4, 4, 16, 16, 16, 16, 16, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 37, 37, 111] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 253 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342440231 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440231 Building ZINC001342440245 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342440245 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/885 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCNC[C@@H]1CO) `ZINC001342440245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342440245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342440245 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCNC[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 3, 16, 16, 21, 21, 21, 21, 21, 21, 21, 35, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 35, 35, 105] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 250 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/886 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCNC[C@@H]1CO) `ZINC001342440245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342440245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342440245 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCNC[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 17, 17, 8, 17, 17, 4, 4, 1, 1, 1, 3, 13, 13, 16, 16, 16, 16, 16, 16, 16, 26, 4, 4, 4, 17, 17, 8, 17, 17, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 26, 26, 78] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342440245 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245 Building ZINC001342440245 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342440245 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 885) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCNC[C@@H]1CO) `ZINC001342440245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342440245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342440245 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCNC[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 3, 16, 16, 21, 21, 21, 21, 21, 21, 21, 35, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 35, 35, 105] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 250 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 886) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCNC[C@@H]1CO) `ZINC001342440245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342440245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001342440245 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCNC[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 17, 17, 8, 17, 17, 4, 4, 1, 1, 1, 3, 13, 13, 16, 16, 16, 16, 16, 16, 16, 26, 4, 4, 4, 17, 17, 8, 17, 17, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 26, 26, 78] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342440245 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342440245 Building ZINC001342487968 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342487968 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/887 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001342487968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342487968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487968 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 8, 30, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/888 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/888' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001342487968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342487968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487968 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 7, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342487968 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968 Building ZINC001342487968 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342487968 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 887) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001342487968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342487968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487968 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 8, 30, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 888) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001342487968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342487968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487968 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 7, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342487968 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487968 Building ZINC001342487972 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342487972 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/889 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC001342487972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342487972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487972 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/890 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC001342487972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342487972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487972 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342487972 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972 Building ZINC001342487972 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342487972 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 889) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC001342487972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342487972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487972 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 890) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC001342487972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342487972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487972 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342487972 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487972 Building ZINC001342487976 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342487976 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/891 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001342487976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342487976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487976 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/892 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001342487976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342487976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487976 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5, 5, 4, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342487976 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976 Building ZINC001342487976 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342487976 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 891) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001342487976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342487976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487976 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 892) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001342487976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342487976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487976 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5, 5, 4, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342487976 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487976 Building ZINC001342487980 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342487980 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/893 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC001342487980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342487980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487980 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 30, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/894 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC001342487980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342487980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487980 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 6, 29, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5, 5, 4, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342487980 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980 Building ZINC001342487980 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342487980 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 893) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC001342487980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342487980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487980 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 30, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 894) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC001342487980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342487980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001342487980 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 6, 29, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5, 5, 4, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342487980 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342487980 Building ZINC001342603286 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342603286 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/895 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)cc1) `ZINC001342603286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342603286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001342603286 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 3, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/2379/xbv-8058097.48/working/building/ZINC001342603286 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/896 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)cc1) `ZINC001342603286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342603286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001342603286 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 4, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342603286 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286 Building ZINC001342603286 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342603286 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 895) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)cc1) `ZINC001342603286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342603286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001342603286 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 3, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/2379/xbv-8058097.48/working/building/ZINC001342603286 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 896) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)cc1) `ZINC001342603286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342603286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001342603286 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC3(CCNCC3)C(=O)O2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 4, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342603286 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603286 Building ZINC001342603288 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342603288 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/897 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)cc1) `ZINC001342603288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342603288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001342603288 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/898 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)cc1) `ZINC001342603288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342603288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001342603288 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 4, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342603288 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288 Building ZINC001342603288 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342603288 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 897) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)cc1) `ZINC001342603288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342603288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001342603288 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 898) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)cc1) `ZINC001342603288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342603288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001342603288 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC3(CCNCC3)C(=O)O2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 1, 11, 12, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 4, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342603288 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342603288 Building ZINC001342720352 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342720352 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/899 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNCCNCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001342720352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342720352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001342720352 none O=C(N1CCNCCNCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 7, 7, 7, 16, 16, 8, 16, 16, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/900 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNCCNCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001342720352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342720352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001342720352 none O=C(N1CCNCCNCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 18, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 9, 9, 19, 19, 9, 19, 19, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 19, 19, 10, 19, 19, 9] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342720352 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352 Building ZINC001342720352 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342720352 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 899) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: O=C(N1CCNCCNCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001342720352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342720352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001342720352 none O=C(N1CCNCCNCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 7, 7, 7, 16, 16, 8, 16, 16, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 900) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: O=C(N1CCNCCNCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001342720352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342720352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001342720352 none O=C(N1CCNCCNCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 18, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 9, 9, 19, 19, 9, 19, 19, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 19, 19, 10, 19, 19, 9] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342720352 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342720352 Building ZINC001342733118 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342733118 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/901 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(C)=O) `ZINC001342733118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342733118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342733118 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 19, 37, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 24, 24, 35, 34, 50, 50, 50] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/902 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/902' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(C)=O) `ZINC001342733118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342733118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342733118 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 20, 19, 44, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 20, 20, 27, 27, 38, 39, 50, 50, 50] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342733118 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118 Building ZINC001342733118 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342733118 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 901) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(C)=O) `ZINC001342733118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342733118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342733118 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 19, 37, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 24, 24, 35, 34, 50, 50, 50] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 902) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(C)=O) `ZINC001342733118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342733118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342733118 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 20, 19, 44, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 20, 20, 27, 27, 38, 39, 50, 50, 50] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342733118 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342733118 Building ZINC001342747360 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342747360 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/903 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)SC) `ZINC001342747360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342747360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342747360 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 24, 42, 42, 42, 50, 17, 17, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 24, 42, 42, 42, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/904 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/904' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)SC) `ZINC001342747360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342747360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342747360 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 18, 18, 18, 43, 43, 43, 50, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 43, 43, 43, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342747360 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360 Building ZINC001342747360 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342747360 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 903) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)SC) `ZINC001342747360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342747360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342747360 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 24, 42, 42, 42, 50, 17, 17, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 24, 42, 42, 42, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 904) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)SC) `ZINC001342747360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342747360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342747360 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 18, 18, 18, 43, 43, 43, 50, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 43, 43, 43, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342747360 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747360 Building ZINC001342747364 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342747364 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/905 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)SC) `ZINC001342747364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342747364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342747364 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 4, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 23, 23, 23, 42, 42, 42, 50, 18, 18, 18, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 23, 42, 42, 42, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 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/2379/xbv-8058097.48/working/building/ZINC001342747364 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/906 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/906' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)SC) `ZINC001342747364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342747364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342747364 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 43, 43, 43, 50, 14, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 19, 43, 43, 43, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 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/2379/xbv-8058097.48/working/building/ZINC001342747364 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342747364 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364 Building ZINC001342747364 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342747364 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 905) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)SC) `ZINC001342747364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342747364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342747364 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 4, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 23, 23, 23, 42, 42, 42, 50, 18, 18, 18, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 23, 42, 42, 42, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 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/2379/xbv-8058097.48/working/building/ZINC001342747364 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 906) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)SC) `ZINC001342747364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342747364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342747364 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 43, 43, 43, 50, 14, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 19, 43, 43, 43, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 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/2379/xbv-8058097.48/working/building/ZINC001342747364 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342747364 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342747364 Building ZINC001342804257 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342804257 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/907 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342804257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342804257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342804257 none COC[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 43, 43, 14, 14, 6, 6, 6, 6, 4, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 50, 50, 50, 50, 50, 43, 43, 43, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/908 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/908' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342804257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342804257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342804257 none COC[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 13, 44, 44, 13, 13, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 50, 50, 50, 50, 50, 44, 44, 44, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342804257 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257 Building ZINC001342804257 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342804257 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 907) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342804257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342804257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342804257 none COC[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 43, 43, 14, 14, 6, 6, 6, 6, 4, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 50, 50, 50, 50, 50, 43, 43, 43, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 908) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342804257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342804257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342804257 none COC[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 13, 44, 44, 13, 13, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 50, 50, 50, 50, 50, 44, 44, 44, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342804257 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804257 Building ZINC001342804259 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342804259 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/909 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342804259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342804259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342804259 none COC[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 14, 44, 44, 14, 14, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 50, 50, 50, 49, 49, 44, 44, 44, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/910 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/910' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342804259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342804259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342804259 none COC[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 46, 46, 15, 15, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 50, 50, 50, 50, 50, 46, 46, 46, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342804259 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259 Building ZINC001342804259 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342804259 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 909) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342804259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342804259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342804259 none COC[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 14, 44, 44, 14, 14, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 50, 50, 50, 49, 49, 44, 44, 44, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 910) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COC[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342804259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342804259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342804259 none COC[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 46, 46, 15, 15, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 50, 50, 50, 50, 50, 46, 46, 46, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342804259 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342804259 Building ZINC001342809319 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342809319 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/911 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cccc(C)n2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342809319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342809319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001342809319 none CO[C@@H]1CN(C(=O)c2cccc(C)n2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 26, 26, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/912 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cccc(C)n2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342809319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342809319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001342809319 none CO[C@@H]1CN(C(=O)c2cccc(C)n2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 14, 14, 14, 14, 14, 25, 25, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342809319 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319 Building ZINC001342809319 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342809319 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 911) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)c2cccc(C)n2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342809319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342809319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001342809319 none CO[C@@H]1CN(C(=O)c2cccc(C)n2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 26, 26, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 912) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)c2cccc(C)n2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342809319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342809319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001342809319 none CO[C@@H]1CN(C(=O)c2cccc(C)n2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 14, 14, 14, 14, 14, 25, 25, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342809319 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809319 Building ZINC001342809577 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342809577 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/913 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2nccc(C)n2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342809577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342809577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001342809577 none CO[C@@H]1CN(C(=O)c2nccc(C)n2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 1, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 10, 10, 10, 10, 10, 17, 17, 50, 50, 29, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 10, 10, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/914 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/914' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2nccc(C)n2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342809577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342809577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001342809577 none CO[C@@H]1CN(C(=O)c2nccc(C)n2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 1, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 9, 9, 15, 15, 50, 50, 38, 50, 50, 50, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 9, 9, 50, 45, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342809577 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577 Building ZINC001342809577 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342809577 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 913) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)c2nccc(C)n2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342809577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342809577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001342809577 none CO[C@@H]1CN(C(=O)c2nccc(C)n2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 1, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 10, 10, 10, 10, 10, 17, 17, 50, 50, 29, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 10, 10, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 914) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)c2nccc(C)n2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342809577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342809577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001342809577 none CO[C@@H]1CN(C(=O)c2nccc(C)n2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 1, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 9, 9, 15, 15, 50, 50, 38, 50, 50, 50, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 9, 9, 50, 45, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342809577 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809577 Building ZINC001342809739 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342809739 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/915 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2nc(C)c[nH]2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342809739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342809739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001342809739 none CO[C@@H]1CN(C(=O)c2nc(C)c[nH]2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 1, 5, 1, 8, 6, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 14, 14, 14, 14, 14, 36, 36, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 14, 14, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/916 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/916' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2nc(C)c[nH]2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342809739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342809739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001342809739 none CO[C@@H]1CN(C(=O)c2nc(C)c[nH]2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 1, 5, 1, 8, 6, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 15, 15, 15, 15, 15, 35, 35, 50, 50, 50, 50, 50, 50, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 15, 15, 50, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342809739 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739 Building ZINC001342809739 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342809739 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 915) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)c2nc(C)c[nH]2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342809739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342809739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001342809739 none CO[C@@H]1CN(C(=O)c2nc(C)c[nH]2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 1, 5, 1, 8, 6, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 14, 14, 14, 14, 14, 36, 36, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 14, 14, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 916) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)c2nc(C)c[nH]2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342809739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342809739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001342809739 none CO[C@@H]1CN(C(=O)c2nc(C)c[nH]2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 1, 5, 1, 8, 6, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 15, 15, 15, 15, 15, 35, 35, 50, 50, 50, 50, 50, 50, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 15, 15, 50, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342809739 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342809739 Building ZINC001342810066 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001342810066 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/917 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 45, 37, 45, 12, 7, 12, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 7, 50, 50, 50, 50, 50, 49, 49, 45, 45, 45, 37, 37, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/918 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/918' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 45, 37, 45, 12, 7, 12, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 7, 50, 50, 50, 50, 50, 49, 49, 45, 45, 45, 37, 37, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/919 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/919' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 47, 36, 47, 13, 7, 13, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 7, 50, 50, 50, 50, 50, 48, 48, 47, 47, 47, 36, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/920 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/920' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 47, 36, 47, 13, 7, 13, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 7, 50, 50, 50, 50, 50, 48, 48, 47, 47, 47, 36, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342810066 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 Building ZINC001342810066 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001342810066 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 917) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 45, 37, 45, 12, 7, 12, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 7, 50, 50, 50, 50, 50, 49, 49, 45, 45, 45, 37, 37, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 918) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 45, 37, 45, 12, 7, 12, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 7, 50, 50, 50, 50, 50, 49, 49, 45, 45, 45, 37, 37, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 919) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 47, 36, 47, 13, 7, 13, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 7, 50, 50, 50, 50, 50, 48, 48, 47, 47, 47, 36, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 920) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 47, 36, 47, 13, 7, 13, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 7, 50, 50, 50, 50, 50, 48, 48, 47, 47, 47, 36, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342810066 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 Building ZINC001342810066 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001342810066 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 917) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 45, 37, 45, 12, 7, 12, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 7, 50, 50, 50, 50, 50, 49, 49, 45, 45, 45, 37, 37, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 918) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 45, 37, 45, 12, 7, 12, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 7, 50, 50, 50, 50, 50, 49, 49, 45, 45, 45, 37, 37, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 919) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 47, 36, 47, 13, 7, 13, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 7, 50, 50, 50, 50, 50, 48, 48, 47, 47, 47, 36, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 920) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 47, 36, 47, 13, 7, 13, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 7, 50, 50, 50, 50, 50, 48, 48, 47, 47, 47, 36, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342810066 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 Building ZINC001342810066 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001342810066 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 917) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 45, 37, 45, 12, 7, 12, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 7, 50, 50, 50, 50, 50, 49, 49, 45, 45, 45, 37, 37, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 918) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 45, 37, 45, 12, 7, 12, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 7, 50, 50, 50, 50, 50, 49, 49, 45, 45, 45, 37, 37, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `2' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/2 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 2 (index: 919) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 47, 36, 47, 13, 7, 13, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 7, 50, 50, 50, 50, 50, 48, 48, 47, 47, 47, 36, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `3' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/3 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 3 (index: 920) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810066.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001342810066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001342810066 none CCCN(C)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 47, 36, 47, 13, 7, 13, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 7, 50, 50, 50, 50, 50, 48, 48, 47, 47, 47, 36, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342810066 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 3: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/3.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/0.* 2: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/2.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810066 Building ZINC001342810140 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342810140 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/921 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342810140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001342810140 none CCCCOCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 23, 17, 5, 5, 5, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 50, 50, 50, 50, 50, 50, 50, 30, 30, 17, 17, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/922 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/922' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342810140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001342810140 none CCCCOCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 25, 20, 10, 10, 10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 50, 50, 50, 50, 50, 50, 50, 31, 31, 20, 20, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342810140 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140 Building ZINC001342810140 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342810140 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 921) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCCCOCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342810140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001342810140 none CCCCOCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 23, 17, 5, 5, 5, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 50, 50, 50, 50, 50, 50, 50, 30, 30, 17, 17, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 922) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCCCOCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342810140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001342810140 none CCCCOCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 25, 20, 10, 10, 10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 50, 50, 50, 50, 50, 50, 50, 31, 31, 20, 20, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342810140 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342810140 Building ZINC001342811459 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342811459 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/923 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cncs2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342811459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342811459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001342811459 none CO[C@@H]1CN(C(=O)c2cncs2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.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'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 23, 23, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/924 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/924' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cncs2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342811459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342811459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001342811459 none CO[C@@H]1CN(C(=O)c2cncs2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.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'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 11, 11, 11, 11, 21, 21, 50, 50, 50, 50, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 11, 11, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342811459 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459 Building ZINC001342811459 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342811459 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 923) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)c2cncs2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342811459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342811459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001342811459 none CO[C@@H]1CN(C(=O)c2cncs2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.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'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 23, 23, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 924) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)c2cncs2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342811459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342811459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001342811459 none CO[C@@H]1CN(C(=O)c2cncs2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.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'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 11, 11, 11, 11, 21, 21, 50, 50, 50, 50, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 11, 11, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342811459 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811459 Building ZINC001342811514 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342811514 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/925 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccc(C)n2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342811514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342811514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001342811514 none CO[C@@H]1CN(C(=O)c2ccc(C)n2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 13, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/926 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/926' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccc(C)n2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342811514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342811514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001342811514 none CO[C@@H]1CN(C(=O)c2ccc(C)n2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342811514 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514 Building ZINC001342811514 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342811514 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 925) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)c2ccc(C)n2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342811514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342811514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001342811514 none CO[C@@H]1CN(C(=O)c2ccc(C)n2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 13, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 926) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)c2ccc(C)n2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342811514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342811514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001342811514 none CO[C@@H]1CN(C(=O)c2ccc(C)n2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342811514 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811514 Building ZINC001342811710 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342811710 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/927 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC(F)(F)F)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342811710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342811710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001342811710 none CO[C@@H]1CN(C(=O)CC(F)(F)F)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 15, 15, 15, 15, 27, 27, 50, 50, 50, 50, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 15, 15, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/928 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/928' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC(F)(F)F)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342811710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342811710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001342811710 none CO[C@@H]1CN(C(=O)CC(F)(F)F)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 21, 21, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 13, 13, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342811710 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710 Building ZINC001342811710 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342811710 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 927) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)CC(F)(F)F)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342811710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342811710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001342811710 none CO[C@@H]1CN(C(=O)CC(F)(F)F)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 15, 15, 15, 15, 27, 27, 50, 50, 50, 50, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 15, 15, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 928) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)CC(F)(F)F)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342811710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342811710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001342811710 none CO[C@@H]1CN(C(=O)CC(F)(F)F)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 21, 21, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 13, 13, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342811710 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342811710 Building ZINC001342812270 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342812270 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/929 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)Cc2cccnc2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342812270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342812270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001342812270 none CO[C@@H]1CN(C(=O)Cc2cccnc2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 10, 10, 10, 10, 10, 17, 17, 42, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 10, 10, 42, 42, 50, 50, 50, 50, 10, 10, 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: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/930 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/930' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)Cc2cccnc2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342812270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342812270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001342812270 none CO[C@@H]1CN(C(=O)Cc2cccnc2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 15, 15, 40, 50, 50, 50, 50, 50, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 9, 9, 40, 40, 50, 50, 50, 50, 9, 9, 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342812270 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270 Building ZINC001342812270 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342812270 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 929) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)Cc2cccnc2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342812270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342812270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001342812270 none CO[C@@H]1CN(C(=O)Cc2cccnc2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 10, 10, 10, 10, 10, 17, 17, 42, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 10, 10, 42, 42, 50, 50, 50, 50, 10, 10, 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: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 930) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CO[C@@H]1CN(C(=O)Cc2cccnc2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342812270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342812270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001342812270 none CO[C@@H]1CN(C(=O)Cc2cccnc2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 15, 15, 40, 50, 50, 50, 50, 50, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 9, 9, 40, 40, 50, 50, 50, 50, 9, 9, 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001342812270 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001342812270 Building ZINC001343170409 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343170409 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/931 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343170409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343170409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001343170409 none CC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 50, 19, 23, 5, 5, 5, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 39, 39, 29, 29, 23, 23, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 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, 48]) total number of confs: 257 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/932 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/932' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343170409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343170409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001343170409 none CC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 50, 17, 15, 4, 4, 4, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 37, 37, 23, 23, 15, 15, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 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, 48]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343170409 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409 Building ZINC001343170409 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343170409 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 931) grep: /scratch/xiaobo/2379/xbv-8058097.48/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(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343170409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343170409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001343170409 none CC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 50, 19, 23, 5, 5, 5, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 39, 39, 29, 29, 23, 23, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 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, 48]) total number of confs: 257 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 932) grep: /scratch/xiaobo/2379/xbv-8058097.48/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(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343170409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343170409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001343170409 none CC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 50, 17, 15, 4, 4, 4, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 37, 37, 23, 23, 15, 15, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 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, 48]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343170409 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343170409 Building ZINC001343181963 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343181963 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/933 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)SCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343181963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343181963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343181963 none CC(C)SCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 37, 8, 8, 8, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 37, 37, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/934 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/934' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)SCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343181963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343181963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343181963 none CC(C)SCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 38, 12, 12, 12, 7, 7, 7, 7, 5, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343181963 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963 Building ZINC001343181963 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343181963 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 933) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)SCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343181963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343181963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343181963 none CC(C)SCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 37, 8, 8, 8, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 37, 37, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 934) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)SCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343181963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343181963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343181963 none CC(C)SCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 38, 12, 12, 12, 7, 7, 7, 7, 5, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343181963 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343181963 Building ZINC001343188054 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343188054 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/935 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@H]2CCCO2)[C@@H](O)C1) `ZINC001343188054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343188054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343188054 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 7, 7, 7, 7, 12, 12, 12, 34, 47, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 34, 34, 46, 46, 50, 50, 50, 50, 50, 50, 21, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/936 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@H]2CCCO2)[C@@H](O)C1) `ZINC001343188054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343188054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343188054 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 5, 6, 6, 6, 6, 10, 10, 10, 32, 44, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 32, 32, 42, 42, 50, 50, 50, 50, 50, 50, 18, 6, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343188054 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054 Building ZINC001343188054 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343188054 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 935) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@H]2CCCO2)[C@@H](O)C1) `ZINC001343188054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343188054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343188054 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 7, 7, 7, 7, 12, 12, 12, 34, 47, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 34, 34, 46, 46, 50, 50, 50, 50, 50, 50, 21, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 936) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@H]2CCCO2)[C@@H](O)C1) `ZINC001343188054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343188054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343188054 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 5, 6, 6, 6, 6, 10, 10, 10, 32, 44, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 32, 32, 42, 42, 50, 50, 50, 50, 50, 50, 18, 6, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343188054 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188054 Building ZINC001343188055 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343188055 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/937 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@@H]2CCCO2)[C@@H](O)C1) `ZINC001343188055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343188055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343188055 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 8, 8, 8, 11, 11, 11, 31, 43, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 11, 31, 31, 41, 41, 50, 50, 50, 50, 50, 50, 24, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/938 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/938' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@@H]2CCCO2)[C@@H](O)C1) `ZINC001343188055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343188055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343188055 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 7, 7, 7, 30, 44, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 30, 30, 40, 40, 50, 50, 50, 50, 50, 50, 12, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343188055 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055 Building ZINC001343188055 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343188055 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 937) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@@H]2CCCO2)[C@@H](O)C1) `ZINC001343188055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343188055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343188055 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 8, 8, 8, 11, 11, 11, 31, 43, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 11, 31, 31, 41, 41, 50, 50, 50, 50, 50, 50, 24, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 938) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@@H]2CCCO2)[C@@H](O)C1) `ZINC001343188055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343188055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343188055 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CC[C@@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 7, 7, 7, 30, 44, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 30, 30, 40, 40, 50, 50, 50, 50, 50, 50, 12, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343188055 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343188055 Building ZINC001343268632 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268632 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/939 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(C)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343268632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001343268632 none CC(C)C(C)(C)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 29, 50, 50, 17, 29, 17, 17, 6, 17, 4, 1, 4, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 51, 17, 17] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 243 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/940 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(C)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343268632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001343268632 none CC(C)C(C)(C)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 27, 49, 49, 15, 27, 15, 15, 5, 15, 3, 1, 3, 1, 1, 1, 2, 2, 2, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 15, 15, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 45, 15, 15] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 245 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343268632 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632 Building ZINC001343268632 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268632 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 939) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)(C)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343268632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001343268632 none CC(C)C(C)(C)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 29, 50, 50, 17, 29, 17, 17, 6, 17, 4, 1, 4, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 51, 17, 17] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 243 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 940) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)(C)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343268632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001343268632 none CC(C)C(C)(C)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 27, 49, 49, 15, 27, 15, 15, 5, 15, 3, 1, 3, 1, 1, 1, 2, 2, 2, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 15, 15, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 45, 15, 15] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 245 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343268632 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268632 Building ZINC001343268671 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268671 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/941 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCO1) `ZINC001343268671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343268671 none CC1=C(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 12, 32, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/942 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/942' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCO1) `ZINC001343268671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343268671 none CC1=C(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 30, 12, 30, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343268671 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671 Building ZINC001343268671 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268671 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 941) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC1=C(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCO1) `ZINC001343268671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343268671 none CC1=C(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 12, 32, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 942) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC1=C(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCO1) `ZINC001343268671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343268671 none CC1=C(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 30, 12, 30, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343268671 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268671 Building ZINC001343268673 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268673 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/943 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343268673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343268673 none CC(C)C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 35, 35, 35, 35, 14, 35, 9, 14, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/944 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/944' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343268673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343268673 none CC(C)C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 38, 38, 38, 38, 14, 38, 9, 14, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343268673 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673 Building ZINC001343268673 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268673 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 943) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343268673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343268673 none CC(C)C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 35, 35, 35, 35, 14, 35, 9, 14, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 944) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343268673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343268673 none CC(C)C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 38, 38, 38, 38, 14, 38, 9, 14, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343268673 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268673 Building ZINC001343268703 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268703 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/945 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343268703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001343268703 none COCCCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 26, 23, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 32, 32, 28, 28, 23, 23, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 253 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/946 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343268703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001343268703 none COCCCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 21, 17, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 28, 28, 24, 24, 17, 17, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343268703 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703 Building ZINC001343268703 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268703 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 945) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343268703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001343268703 none COCCCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 26, 23, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 32, 32, 28, 28, 23, 23, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 253 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 946) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCCCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343268703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001343268703 none COCCCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 21, 17, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 28, 28, 24, 24, 17, 17, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343268703 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268703 Building ZINC001343268825 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268825 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/947 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccccc2)C[C@@H]1O) `ZINC001343268825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343268825 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccccc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 19, 19, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 207 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/948 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccccc2)C[C@@H]1O) `ZINC001343268825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343268825 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccccc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 19, 19, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343268825 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825 Building ZINC001343268825 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268825 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 947) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccccc2)C[C@@H]1O) `ZINC001343268825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343268825 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccccc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 19, 19, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 207 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 948) grep: /scratch/xiaobo/2379/xbv-8058097.48/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)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccccc2)C[C@@H]1O) `ZINC001343268825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343268825 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccccc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 19, 19, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343268825 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343268825 Building ZINC001343269127 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269127 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/949 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H](CC)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343269127 none CCO[C@H](CC)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 43, 18, 43, 43, 46, 10, 18, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 273 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/950 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/950' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H](CC)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343269127 none CCO[C@H](CC)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 45, 19, 45, 45, 45, 9, 19, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 284 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269127 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127 Building ZINC001343269127 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269127 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 949) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H](CC)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343269127 none CCO[C@H](CC)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 43, 18, 43, 43, 46, 10, 18, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 273 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 950) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@H](CC)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343269127 none CCO[C@H](CC)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 45, 19, 45, 45, 45, 9, 19, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 284 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269127 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269127 Building ZINC001343269128 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269128 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/951 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H](CC)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343269128 none CCO[C@@H](CC)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 44, 22, 44, 44, 45, 13, 22, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 266 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/952 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H](CC)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343269128 none CCO[C@@H](CC)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 19, 43, 43, 46, 9, 19, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 274 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269128 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128 Building ZINC001343269128 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269128 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 951) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@@H](CC)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343269128 none CCO[C@@H](CC)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 44, 22, 44, 44, 45, 13, 22, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 266 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 952) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCO[C@@H](CC)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343269128 none CCO[C@@H](CC)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 19, 43, 43, 46, 9, 19, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 274 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269128 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269128 Building ZINC001343269213 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269213 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/953 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001343269213 none Cc1ccsc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 33, 12, 33, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 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]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/954 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/954' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001343269213 none Cc1ccsc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 34, 12, 34, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 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]) total number of confs: 161 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269213 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213 Building ZINC001343269213 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269213 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 953) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccsc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001343269213 none Cc1ccsc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 33, 12, 33, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 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]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 954) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccsc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001343269213 none Cc1ccsc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 34, 12, 34, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 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]) total number of confs: 161 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269213 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269213 Building ZINC001343269239 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269239 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/955 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343269239 none CC[C@@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 15, 15, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 34, 20, 34, 34, 44, 50, 50, 12, 20, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 41, 41, 41, 41, 41, 46, 46, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 322 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/956 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343269239 none CC[C@@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 15, 15, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 32, 18, 32, 32, 44, 50, 50, 9, 18, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 40, 40, 40, 40, 40, 46, 46, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 337 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269239 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239 Building ZINC001343269239 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269239 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 955) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC[C@@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343269239 none CC[C@@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 15, 15, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 34, 20, 34, 34, 44, 50, 50, 12, 20, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 41, 41, 41, 41, 41, 46, 46, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 322 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 956) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC[C@@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343269239 none CC[C@@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 15, 15, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 32, 18, 32, 32, 44, 50, 50, 9, 18, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 40, 40, 40, 40, 40, 46, 46, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 337 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269239 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269239 Building ZINC001343269242 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269242 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/957 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343269242 none CC[C@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 15, 15, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 37, 21, 37, 37, 46, 50, 50, 12, 21, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 41, 41, 41, 41, 41, 49, 49, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/958 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/958' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343269242 none CC[C@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 15, 15, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 30, 16, 30, 30, 44, 50, 50, 11, 16, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 38, 38, 38, 38, 38, 47, 47, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 336 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269242 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242 Building ZINC001343269242 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269242 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 957) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC[C@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343269242 none CC[C@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 15, 15, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 37, 21, 37, 37, 46, 50, 50, 12, 21, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 41, 41, 41, 41, 41, 49, 49, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 958) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC[C@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343269242 none CC[C@H](CC(F)F)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 15, 15, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 30, 16, 30, 30, 44, 50, 50, 11, 16, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 38, 38, 38, 38, 38, 47, 47, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 336 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269242 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269242 Building ZINC001343269260 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269260 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/959 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)o1) `ZINC001343269260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343269260 none Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 12, 30, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/960 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/960' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)o1) `ZINC001343269260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343269260 none Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 157 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269260 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260 Building ZINC001343269260 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269260 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 959) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)o1) `ZINC001343269260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343269260 none Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 12, 30, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 960) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)o1) `ZINC001343269260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343269260 none Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 157 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269260 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269260 Building ZINC001343269296 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269296 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/961 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCC(F)(F)C2)C[C@@H]1O) `ZINC001343269296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343269296 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCC(F)(F)C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 15, 15, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 23, 23, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 188 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/962 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/962' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCC(F)(F)C2)C[C@@H]1O) `ZINC001343269296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343269296 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCC(F)(F)C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 15, 15, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 22, 22, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 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: 180 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269296 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296 Building ZINC001343269296 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269296 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 961) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCC(F)(F)C2)C[C@@H]1O) `ZINC001343269296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343269296 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCC(F)(F)C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 15, 15, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 23, 23, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 188 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 962) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCC(F)(F)C2)C[C@@H]1O) `ZINC001343269296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343269296 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCC(F)(F)C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 15, 15, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 22, 22, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 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: 180 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269296 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269296 Building ZINC001343269298 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269298 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/963 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCC(F)(F)C2)C[C@@H]1O) `ZINC001343269298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343269298 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCC(F)(F)C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 15, 15, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 21, 21, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/964 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/964' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCC(F)(F)C2)C[C@@H]1O) `ZINC001343269298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343269298 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCC(F)(F)C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 15, 15, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 23, 23, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269298 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298 Building ZINC001343269298 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269298 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 963) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCC(F)(F)C2)C[C@@H]1O) `ZINC001343269298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343269298 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCC(F)(F)C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 15, 15, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 21, 21, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 964) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCC(F)(F)C2)C[C@@H]1O) `ZINC001343269298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343269298 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCC(F)(F)C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 15, 15, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 23, 23, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269298 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269298 Building ZINC001343269766 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269766 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/965 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCC(F)(F)F)C[C@@H]1O) `ZINC001343269766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343269766 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCC(F)(F)F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 15, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 18, 18, 48, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 48, 48, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 229 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/966 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/966' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCC(F)(F)F)C[C@@H]1O) `ZINC001343269766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343269766 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCC(F)(F)F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 15, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 17, 17, 48, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 48, 48, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269766 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766 Building ZINC001343269766 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269766 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 965) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCC(F)(F)F)C[C@@H]1O) `ZINC001343269766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343269766 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCC(F)(F)F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 15, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 18, 18, 48, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 48, 48, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 229 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 966) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCC(F)(F)F)C[C@@H]1O) `ZINC001343269766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343269766 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCC(F)(F)F)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 15, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 17, 17, 48, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 48, 48, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343269766 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343269766 Building ZINC001343270103 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270103 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/967 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)o2)C[C@@H]1O) `ZINC001343270103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001343270103 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)o2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 33, 33, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 158 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/968 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/968' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)o2)C[C@@H]1O) `ZINC001343270103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001343270103 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)o2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of 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, 16, 16, 16, 16, 36, 36, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 50, 50, 16, 16, 48] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270103 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103 Building ZINC001343270103 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270103 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 967) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)o2)C[C@@H]1O) `ZINC001343270103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001343270103 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)o2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 33, 33, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 158 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 968) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)o2)C[C@@H]1O) `ZINC001343270103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001343270103 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(Cl)o2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of 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, 16, 16, 16, 16, 36, 36, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 50, 50, 16, 16, 48] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270103 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270103 Building ZINC001343270163 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270163 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/969 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]nc2C2CC2)C[C@@H]1O) `ZINC001343270163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343270163 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]nc2C2CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 22, 22, 43, 43, 43, 43, 43, 43, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 43, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/970 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/970' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]nc2C2CC2)C[C@@H]1O) `ZINC001343270163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343270163 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]nc2C2CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 23, 23, 45, 45, 45, 45, 45, 45, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 45, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270163 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163 Building ZINC001343270163 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270163 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 969) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]nc2C2CC2)C[C@@H]1O) `ZINC001343270163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343270163 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]nc2C2CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 22, 22, 43, 43, 43, 43, 43, 43, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 43, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 970) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]nc2C2CC2)C[C@@H]1O) `ZINC001343270163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343270163 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]nc2C2CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 23, 23, 45, 45, 45, 45, 45, 45, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 45, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270163 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270163 Building ZINC001343270371 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270371 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/971 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001343270371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270371 none COCC1(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 21, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 43, 43, 50, 50, 50, 50, 50, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 43, 43, 43, 43] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/972 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/972' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001343270371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270371 none COCC1(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 23, 6, 5, 6, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 43, 43, 50, 50, 50, 50, 50, 23, 23, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5, 43, 43, 43, 43] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270371 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371 Building ZINC001343270371 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270371 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 971) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCC1(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001343270371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270371 none COCC1(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 21, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 43, 43, 50, 50, 50, 50, 50, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 43, 43, 43, 43] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 972) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COCC1(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001343270371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270371 none COCC1(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 23, 6, 5, 6, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 43, 43, 50, 50, 50, 50, 50, 23, 23, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5, 43, 43, 43, 43] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270371 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270371 Building ZINC001343270468 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270468 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/973 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccnc2)C[C@@H]1O) `ZINC001343270468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001343270468 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccnc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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, 2, 2, 3, 8, 8, 8, 8, 12, 12, 29, 31, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 31, 31, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/974 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/974' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccnc2)C[C@@H]1O) `ZINC001343270468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001343270468 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccnc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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, 2, 2, 3, 10, 10, 10, 10, 13, 13, 31, 33, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 31, 31, 33, 33, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270468 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468 Building ZINC001343270468 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270468 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 973) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccnc2)C[C@@H]1O) `ZINC001343270468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001343270468 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccnc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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, 2, 2, 3, 8, 8, 8, 8, 12, 12, 29, 31, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 31, 31, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 974) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccnc2)C[C@@H]1O) `ZINC001343270468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001343270468 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2cccnc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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, 2, 2, 3, 10, 10, 10, 10, 13, 13, 31, 33, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 31, 31, 33, 33, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270468 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270468 Building ZINC001343270720 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270720 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/975 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCCOC2)C[C@@H]1O) `ZINC001343270720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270720 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCCOC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 8, 19, 19, 19, 19, 35, 47, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 57] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/976 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/976' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCCOC2)C[C@@H]1O) `ZINC001343270720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270720 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCCOC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 18, 18, 18, 18, 34, 44, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 131 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270720 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720 Building ZINC001343270720 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270720 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 975) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCCOC2)C[C@@H]1O) `ZINC001343270720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270720 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCCOC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 8, 19, 19, 19, 19, 35, 47, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 57] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 976) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCCOC2)C[C@@H]1O) `ZINC001343270720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270720 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCCOC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 18, 18, 18, 18, 34, 44, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 131 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270720 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270720 Building ZINC001343270722 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270722 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/977 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCCOC2)C[C@@H]1O) `ZINC001343270722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270722 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCCOC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 32, 41, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/978 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/978' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCCOC2)C[C@@H]1O) `ZINC001343270722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270722 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCCOC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 6, 14, 14, 14, 14, 33, 43, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 179 number of broken/clashed sets: 136 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270722 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722 Building ZINC001343270722 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270722 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 977) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCCOC2)C[C@@H]1O) `ZINC001343270722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270722 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCCOC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 32, 41, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 978) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCCOC2)C[C@@H]1O) `ZINC001343270722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270722 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCCOC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 6, 14, 14, 14, 14, 33, 43, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 179 number of broken/clashed sets: 136 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270722 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270722 Building ZINC001343270759 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270759 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/979 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nc1C) `ZINC001343270759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001343270759 none Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 29, 11, 29, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50] 150 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: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/980 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/980' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nc1C) `ZINC001343270759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001343270759 none Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 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: 153 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270759 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759 Building ZINC001343270759 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270759 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 979) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nc1C) `ZINC001343270759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001343270759 none Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 29, 11, 29, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50] 150 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: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 980) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nc1C) `ZINC001343270759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001343270759 none Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 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: 153 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270759 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270759 Building ZINC001343270762 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270762 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/981 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1) `ZINC001343270762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343270762 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 20, 31, 9, 20, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 50, 50, 50, 50, 50, 31, 31, 31, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 173 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/982 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/982' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1) `ZINC001343270762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343270762 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 18, 31, 9, 18, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 50, 50, 50, 50, 50, 31, 31, 31, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270762 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762 Building ZINC001343270762 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270762 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 981) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1) `ZINC001343270762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343270762 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 20, 31, 9, 20, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 50, 50, 50, 50, 50, 31, 31, 31, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 173 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 982) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1) `ZINC001343270762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343270762 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 18, 31, 9, 18, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 50, 50, 50, 50, 50, 31, 31, 31, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270762 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270762 Building ZINC001343270765 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270765 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/983 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1) `ZINC001343270765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343270765 none C[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 32, 9, 17, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 32, 50, 50, 50, 50, 50, 32, 32, 32, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/984 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/984' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1) `ZINC001343270765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343270765 none C[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 14, 29, 8, 14, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 29, 50, 50, 50, 50, 50, 29, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270765 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765 Building ZINC001343270765 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270765 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 983) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1) `ZINC001343270765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343270765 none C[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 32, 9, 17, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 32, 50, 50, 50, 50, 50, 32, 32, 32, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 984) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: C[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1) `ZINC001343270765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343270765 none C[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 14, 29, 8, 14, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 29, 50, 50, 50, 50, 50, 29, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270765 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270765 Building ZINC001343270954 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270954 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/985 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343270954 none COc1ccccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 45, 50, 50, 29, 11, 29, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/986 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/986' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343270954 none COc1ccccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 50, 50, 31, 12, 31, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270954 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954 Building ZINC001343270954 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270954 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 985) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1ccccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343270954 none COc1ccccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 45, 50, 50, 29, 11, 29, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 986) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: COc1ccccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343270954 none COc1ccccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 50, 50, 31, 12, 31, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270954 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270954 Building ZINC001343270973 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270973 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/987 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2C=CC=CC=C2)C[C@@H]1O) `ZINC001343270973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343270973 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2C=CC=CC=C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 46, 46, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/988 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/988' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2C=CC=CC=C2)C[C@@H]1O) `ZINC001343270973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343270973 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2C=CC=CC=C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 7, 18, 18, 18, 18, 37, 37, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270973 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973 Building ZINC001343270973 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270973 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 987) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2C=CC=CC=C2)C[C@@H]1O) `ZINC001343270973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343270973 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2C=CC=CC=C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 46, 46, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 988) grep: /scratch/xiaobo/2379/xbv-8058097.48/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2C=CC=CC=C2)C[C@@H]1O) `ZINC001343270973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001343270973 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2C=CC=CC=C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 7, 18, 18, 18, 18, 37, 37, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270973 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270973 Building ZINC001343270976 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270976 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/989 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1occc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343270976 none CCc1occc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 36, 36, 36, 21, 9, 21, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 36, 36, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/990 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/990' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1occc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343270976 none CCc1occc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 36, 36, 36, 19, 9, 19, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 36, 36, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270976 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976 Building ZINC001343270976 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270976 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 989) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1occc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343270976 none CCc1occc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 36, 36, 36, 21, 9, 21, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 36, 36, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 990) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1occc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343270976 none CCc1occc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 36, 36, 36, 19, 9, 19, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 36, 36, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343270976 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343270976 Building ZINC001343271388 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271388 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/991 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001343271388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343271388 none CCOCC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 27, 27, 9, 27, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 50, 50, 50, 50, 50, 48, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 27, 27, 27, 27] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/992 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/992' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001343271388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343271388 none CCOCC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 27, 27, 10, 27, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 27, 27, 50, 50, 50, 50, 50, 48, 48, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 27, 27, 27, 27] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 210 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343271388 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388 Building ZINC001343271388 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271388 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 991) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCOCC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001343271388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343271388 none CCOCC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 27, 27, 9, 27, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 50, 50, 50, 50, 50, 48, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 27, 27, 27, 27] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 992) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCOCC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001343271388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343271388 none CCOCC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 27, 27, 10, 27, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 27, 27, 50, 50, 50, 50, 50, 48, 48, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 27, 27, 27, 27] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 210 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343271388 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271388 Building ZINC001343271390 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271390 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/993 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(O)n1) `ZINC001343271390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343271390 none Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 33, 13, 33, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 100] 300 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]) total number of confs: 263 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/994 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/994' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(O)n1) `ZINC001343271390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343271390 none Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 33, 13, 33, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 100] 300 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]) total number of confs: 262 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343271390 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390 Building ZINC001343271390 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271390 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 993) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(O)n1) `ZINC001343271390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343271390 none Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 33, 13, 33, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 100] 300 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]) total number of confs: 263 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 994) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(O)n1) `ZINC001343271390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343271390 none Cc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 33, 13, 33, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 100] 300 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]) total number of confs: 262 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343271390 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271390 Building ZINC001343271635 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271635 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/995 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)oc1C) `ZINC001343271635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343271635 none Cc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)oc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 12, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 12, 31, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/996 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/996' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)oc1C) `ZINC001343271635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343271635 none Cc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)oc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 12, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343271635 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635 Building ZINC001343271635 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271635 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 995) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)oc1C) `ZINC001343271635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343271635 none Cc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)oc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 12, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 12, 31, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 996) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: Cc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)oc1C) `ZINC001343271635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343271635 none Cc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)oc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 12, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343271635 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271635 Building ZINC001343271663 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271663 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/997 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343271663 none CCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need 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, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/998 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/998' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343271663 none CCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need 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, 19, 8, 19, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 34, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 205 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343271663 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663 Building ZINC001343271663 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271663 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 997) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343271663 none CCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need 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, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 998) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343271663 none CCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need 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, 19, 8, 19, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 34, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 205 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343271663 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271663 Building ZINC001343271698 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271698 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/999 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccoc2Cl)C[C@@H]1O) `ZINC001343271698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001343271698 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccoc2Cl)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 12, 1, 16, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 34, 34, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 167 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/2379/xbv-8058097.48/working/3D/1000 `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/1000' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccoc2Cl)C[C@@H]1O) `ZINC001343271698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001343271698 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccoc2Cl)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 12, 1, 16, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 33, 33, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343271698 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698 Building ZINC001343271698 mkdir: created directory `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271698 mkdir: created directory `0' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698/0 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 0 (index: 999) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccoc2Cl)C[C@@H]1O) `ZINC001343271698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001343271698 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccoc2Cl)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 12, 1, 16, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 34, 34, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 167 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 mkdir: created directory `1' /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698/1 /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Protomer 1 (index: 1000) grep: /scratch/xiaobo/2379/xbv-8058097.48/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccoc2Cl)C[C@@H]1O) `ZINC001343271698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001343271698 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccoc2Cl)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 12, 1, 16, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 33, 33, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698 /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Finished preparing ZINC001343271698 Recording results /scratch/xiaobo/2379/xbv-8058097.48/working /scratch/xiaobo/2379/xbv-8058097.48 Appending to /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.* 0: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698/0.* 1: /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698/1.* Removing working files in /scratch/xiaobo/2379/xbv-8058097.48/working/building/ZINC001343271698 /scratch/xiaobo/2379/xbv-8058097.48 Compressing combined databse files /scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/2379/xbv-8058097.48/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/2379/xbv-8058097.48/working/3D/1001' removed directory: `/scratch/xiaobo/2379/xbv-8058097.48/working/3D' rmdir: removing directory, `/scratch/xiaobo/2379/xbv-8058097.48/working/building' rmdir: removing directory, `/scratch/xiaobo/2379/xbv-8058097.48/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/logs `/scratch/xiaobo/2379/xbv-8058097.48' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xbv' `/scratch/xiaobo/2379/xbv-8058097.48/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xbv/finished' `/scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xbv/finished/xbv.db2.gz' removed `/scratch/xiaobo/2379/xbv-8058097.48/finished/xbv.db2.gz' removed directory: `/scratch/xiaobo/2379/xbv-8058097.48/finished' removed directory: `/scratch/xiaobo/2379/xbv-8058097.48'